<div dir="ltr">Hi Thibaut, Vikram, and others:<div><br></div><div>I'd like to try a randomization experiment to further explore my radseq data using DAPC. </div><div><span style="font-family:Arial;font-size:13.333333969116211px"><br></span></div><div><span style="font-family:Arial;font-size:13.333333969116211px">Data structure:</span></div><p class="MsoNormal" style="font-family:arial,sans-serif;font-size:13.333333969116211px"><span style="font-family:Arial">40 individuals in 2 (apriori) populations </span></p><p class="MsoNormal" style="font-family:arial,sans-serif;font-size:13.333333969116211px"><span style="font-family:Arial">6451 SNP loci</span></p><p class="MsoNormal" style="font-family:arial,sans-serif;font-size:13.333333969116211px"><span style="font-family:Arial"><br></span></p><p class="MsoNormal" style="font-family:arial,sans-serif;font-size:13.333333969116211px"><span style="font-family:Arial">My data are for two very closely related "species" which show little to no divergence at traditional markers. I performed a </span><span style="font-family:Arial">DAPC using a priori pop definitions (set as species). The function can discriminate my species, but the</span><span style="font-family:Arial"> allelic contributions are very low ( highest few around .0015). </span></p><p class="MsoNormal" style="font-family:arial,sans-serif;font-size:13.333333969116211px"><span style="font-family:Arial"><br></span></p><p class="MsoNormal" style="font-size:13.333333969116211px"><font face="Arial">I am interested in trying a randomization experiment in which I shuffle the population labels 100 times and then perform DAPC on each of these. </font><span style="font-family:Arial">Ultimately the goal is to compare allelic loadings for the discriminant function generated using true labels vs. randomized labels. </span></p><p class="MsoNormal" style="font-size:13.333333969116211px"><span style="font-family:Arial"><br></span></p><p class="MsoNormal" style="font-size:13.333333969116211px"><font face="Arial">I am fairly new to R. A colleague suggested the general format to create a loop, but could anyone offer a solution that could be implemented with a genind object? Otherwise, I think it would be too labor intensive - I would have to create 100 different structure input files to be converted to genind objects. </font></p><p class="MsoNormal" style="font-size:13.333333969116211px"><br></p><div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14.44444465637207px">nrep<- 100</div><div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14.44444465637207px">results<- list() # or vector/matrix, depending on the case</div><div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14.44444465637207px">For(I in 1:nrep)</div><div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14.44444465637207px">{</div><div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14.44444465637207px"> Rand.labels<- sample(labels)</div><div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14.44444465637207px">## do some analyses and assign relevant results to results</div><div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14.44444465637207px">}</div><p class="MsoNormal" style="font-size:13.333333969116211px"><font face="Arial"><br></font></p><div><span style="font-family:Arial">Thanks,</span></div><div><span style="font-family:Arial">Caroline</span></div><div><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Sep 14, 2014 at 3:45 PM, Jombart, Thibaut <span dir="ltr"><<a href="mailto:t.jombart@imperial.ac.uk" target="_blank">t.jombart@imperial.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><br>
Yes, you need to use:<br>
?genind2hierfstat<br>
<br>
Cheers<br>
Thibaut<br>
<br>
________________________________________<br>
From: Vikram Chhatre [<a href="mailto:crypticlineage@gmail.com">crypticlineage@gmail.com</a>]<br>
Sent: 13 September 2014 21:48<br>
To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>; Jombart, Thibaut<br>
<span class="">Subject: Re: [adegenet-forum] Per locus pairwise Fst<br>
<br>
</span><span class="">Thank you for all the replies. I have been looking at the pp.fst() function in the Hierfstat package. Does the post-seploc data frame need to be converted into something that Hierfstat understands first? The following doesn't seem to work:<br>
<br>
# Use seploc to separate loci:<br>
gen100_seploc <- seploc(gen100_genind, truenames=TRUE, res.type=c('genind', 'matrix')<br>
<br>
# Load Hierfstat<br>
library(hierfstat)<br>
<br>
# Calculate pairwise Fst:<br>
gen100_perLocusPWFst <- lapply(gen100_seploc, pp.fst, diploid=TRUE)<br>
<br>
Error in unique.default(Pop) : unique() applies only to vectors<br>
<br>
</span><span class="">On Sat, Sep 13, 2014 at 2:20 PM, Jombart, Thibaut <<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a><mailto:<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>>> wrote:<br>
<br>
Hi there,<br>
<br>
</span><span class="">yes, this function is not optimized for large datasets. You can use the same approach but using functions from the hierfstat package.<br>
<br>
Cheers<br>
Thibaut<br>
________________________________________<br>
</span><span class="">From: <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a><mailto:<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>> [<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a><mailto:<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>>] on behalf of Vikram Chhatre [<a href="mailto:crypticlineage@gmail.com">crypticlineage@gmail.com</a><mailto:<a href="mailto:crypticlineage@gmail.com">crypticlineage@gmail.com</a>>]<br>
</span><span class="">Sent: 12 September 2014 18:31<br>
</span>To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><mailto:<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>><br>
<span class="">Subject: Re: [adegenet-forum] Per locus pairwise Fst<br>
<br>
I am revisiting this topic due to some technical problems.<br>
<br>
The task at hand is to estimate pairwise Fst matrices for each locus separately.<br>
<br>
# Genind object is stored in:<br>
gen100_genind<br>
<br>
# Use seploc to separate loci:<br>
gen100_seploc <- seploc(gen100_genind, truenames=TRUE, res.type=c('genind', 'matrix')<br>
<br>
# Calculate pairwise Fst:<br>
gen100_perLocusPWFst <- lapply(gen100_seploc, pairwise.fst, res.type=c('dist', 'matrix'), trunames=TRUE)<br>
<br>
For a data set consisting of 30 populations, 20 individuals each, 1000 loci and 2 alleles per locus (1.2 million data points), it takes up to 6 hours to estimate the pairwise Fst matrix with this method.<br>
<br>
Is there any way to speed this up? Should I look into any other packages?<br>
<br>
Many thanks for your time and help.<br>
Vikram<br>
<br>
<br>
<br>
<br>
</span><span class="">On Mon, Jul 14, 2014 at 9:16 AM, Vikram Chhatre <<a href="mailto:crypticlineage@gmail.com">crypticlineage@gmail.com</a><mailto:<a href="mailto:crypticlineage@gmail.com">crypticlineage@gmail.com</a>><mailto:<a href="mailto:crypticlineage@gmail.com">crypticlineage@gmail.com</a><mailto:<a href="mailto:crypticlineage@gmail.com">crypticlineage@gmail.com</a>>>> wrote:<br>
Perfect! Thank you for both solutions.<br>
<br>
V<br>
<br>
<br>
</span><span class="">On Mon, Jul 14, 2014 at 9:13 AM, Jombart, Thibaut <<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a><mailto:<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>><mailto:<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a><mailto:<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>>>> wrote:<br>
<br>
Hi there,<br>
<br>
you can use seploc to separate loci, and lapply over the resulting list using your prefered fst function.<br>
<br>
Cheers<br>
Thibaut<br>
________________________________________<br>
</span>From: <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a><mailto:<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>><mailto:<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a><mailto:<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>>> [<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a><mailto:<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>><mailto:<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a><mailto:<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>>>] on behalf of Vikram Chhatre [<a href="mailto:crypticlineage@gmail.com">crypticlineage@gmail.com</a><mailto:<a href="mailto:crypticlineage@gmail.com">crypticlineage@gmail.com</a>><mailto:<a href="mailto:crypticlineage@gmail.com">crypticlineage@gmail.com</a><mailto:<a href="mailto:crypticlineage@gmail.com">crypticlineage@gmail.com</a>>>]<br>
<span class="">Sent: 14 July 2014 14:01<br>
</span>To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><mailto:<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>><mailto:<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><mailto:<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>>><br>
<span class="im">Subject: [adegenet-forum] Per locus pairwise Fst<br>
<br>
Good morning.<br>
<br>
I would like to estimate per locus pairwise Fst for populations, but it appears that Adegenet only estimates this over all loci (i.e. single matrix). What I would like is one matrix per locus. Has anyone modified the functions or know of alternative programs that can do this?<br>
<br>
Thanks<br>
Vikram<br>
<br>
<br>
<br>
<br>
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