Just under 2000 individuals at just over 6000 SNPs. I'm looking into finding a server to run it on. Shouldn't be too difficult I'd guess.<div><br></div><div>Cheers,</div><div>Grant<br><br><div class="gmail_quote">
On 21 June 2012 16:59, 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Yes, for now, sPCA is not implemented for genlight objects.<br>
<br>
What is the size of your dataset?<br>
<br>
Cheers<br>
<br>
Thibaut<br>
________________________________________<br>
From: Grant Gillis [<a href="mailto:grant.j.gillis@gmail.com">grant.j.gillis@gmail.com</a>]<br>
Sent: 21 June 2012 16:31<br>
To: Jombart, Thibaut<br>
Cc: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
Subject: Re: [adegenet-forum] Reading SNP data as a genind oblect<br>
<div class="im"><br>
Great. Thanks!<br>
<br>
As a follow up. I had hoped to do an spca on my SNP data but it seems to be just too big for the memory. I haven't been able to find out whether it is possible to do an spca on a genlight oblect. It appears not to be. Is this true?<br>
<br>
Many thanks again.<br>
<br>
</div><div class="im">On 21 June 2012 14:26, 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>
Hello,<br>
<br>
the problems comes from the format of the raw data. Two alleles from a given locus should be a single column, possibly with a separator such as "/". Here, alleles are on separate columns.<br>
<br>
Cheers<br>
<br>
Thibaut<br>
<br>
--<br>
######################################<br>
Dr Thibaut JOMBART<br>
MRC Centre for Outbreak Analysis and Modelling<br>
Department of Infectious Disease Epidemiology<br>
Imperial College - School of Public Health<br>
St Mary’s Campus<br>
Norfolk Place<br>
London W2 1PG<br>
United Kingdom<br>
Tel. : 0044 (0)20 7594 3658<br>
</div><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>><br>
<div class="im"><a href="http://sites.google.com/site/thibautjombart/" target="_blank">http://sites.google.com/site/thibautjombart/</a><br>
<a href="http://adegenet.r-forge.r-project.org/" target="_blank">http://adegenet.r-forge.r-project.org/</a><br>
________________________________________<br>
</div>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 Grant Gillis [<a href="mailto:grant.j.gillis@gmail.com">grant.j.gillis@gmail.com</a><mailto:<a href="mailto:grant.j.gillis@gmail.com">grant.j.gillis@gmail.com</a>>]<br>
<div class="im">Sent: 21 June 2012 13:22<br>
</div>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>
<div class="im HOEnZb">Subject: [adegenet-forum] Reading SNP data as a genind oblect<br>
<br>
Dear List,<br>
<br>
I have SNP data structured as below. This seems to be accepted as a genind object however the obj@tab suggests to me something strange is going on. Too many alleles per locus. Any tips as to where I'm going wrong would be much appreciated.<br>
<br>
Cheers,<br>
Grant<br>
<br>
<br>
<br>
> dat <- structure(c("A", "A", "A", "G", "G", "G", "A", "G", "NA", "G",<br>
+ "G", "NA", "A", "A", "A", "A", "G", "A", "A", "C", "A", "A",<br>
+ "C", "C"), .Dim = c(3L, 8L), .Dimnames = list(c("genot. 1", "genot. 2",<br>
+ "genot. 3"), c("1", "1", "2", "2", "3", "3", "4", "4")))<br>
<br>
<br>
1 1 2 2 3 3 4 4<br>
genot. 1 "A" "G" "A" "G" "A" "A" "A" "A"<br>
genot. 2 "A" "G" "G" "G" "A" "G" "C" "C"<br>
genot. 3 "A" "G" "NA" "NA" "A" "A" "A" "C"<br>
><br>
><br>
><br>
<br>
<br>
> obj <- df2genind(dat, ploidy=2, missing = NA)<br>
><br>
><br>
> obj@tab<br>
L1.1 L1.2 L1.3 L1.4 L2.1 L2.2 L2.3 L2.4 L2.5 L3.1 L3.2 L3.3 L3.4 L3.5 L4.1 L4.2 L4.3 L4.4 L4.5 L4.6<br>
1 0.5 0.5 0.5 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.5 0.5 0.5 0.0 0.5 0.5 0.0 0.5 0.5 0.0<br>
2 0.5 0.5 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.5 0.5 0.5 0.0 0.5 0.5 0.0 0.5 0.5 0.0 0.5<br>
3 0.5 0.5 0.5 0.5 NA NA NA NA NA 0.5 0.5 0.5 0.5 0.0 0.5 0.5 0.0 0.5 0.0 0.5<br>
<br>
<br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Colin Garroway<br><p><font><font style="color:rgb(0,0,0);font-family:arial,sans-serif" size="2">Edward Grey Institute,</font></font><br><font><font style="color:rgb(0,0,0);font-family:arial,sans-serif" size="2">Department of Zoology,<br>
South Parks Road,<br>University of Oxford,<br>OX1 3PS</font></font></p><a href="http://sites.google.com/site/colingarroway2/home" target="_blank">http://sites.google.com/site/colingarroway2/home</a><br><br>
</div>