<div dir="ltr"><div><br><br></div>Patrícia,<br><br>About this same subject I would like to recommend you an article I've read some time ago.<br><br>Reference:<br>Kalinowski, ST (2011) "The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure", Heredity, 106 :625-632<br>
<br>Cheers,<br>M.<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-06-14 17:00 GMT+01:00 Manuela <span dir="ltr"><<a href="mailto:manuelacorreia2@gmail.com" target="_blank">manuelacorreia2@gmail.com</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>Sorry, I meant DAPC tutorial (March 24,2014).<br><br></div>Cheers,<br></div>M.<br></div><div class="gmail_extra">
<br><br><div class="gmail_quote">2014-06-14 16:56 GMT+01:00 Manuela <span dir="ltr"><<a href="mailto:manuelacorreia2@gmail.com" target="_blank">manuelacorreia2@gmail.com</a>></span>:<div><div class="h5"><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">
<p class="MsoNormal"><span lang="EN-US">Patrícia,</span></p>
<p class="MsoNormal"><span lang="EN-US"><br></span></p><p class="MsoNormal"><span lang="EN-US"><br></span></p><p class="MsoNormal"><span lang="EN-US">I made a
small test with example suggested on sPCA tutorial (<a href="http://adegenet.r-forge.r-project.org/" target="_blank">http://adegenet.r-forge.r-project.org/</a>)
and apparently it seems that you can get the SNP loadings after modelling yout
dataset by DAPC. The values you want are stored in the slot pca.loadings. <br></span></p><p class="MsoNormal"><span lang="EN-US"><br></span></p>
<p class="MsoNormal"><span lang="EN-US">Just try these two
command lines: </span></p>
<p class="MsoNormal"><span lang="EN-US">A<-dapc1$pca.loadings</span></p>
<p class="MsoNormal"><span lang="EN-US">write.table(A,file=”A”)</span></p>
<p class="MsoNormal"><span lang="EN-US"><br></span></p><p class="MsoNormal"><span lang="EN-US">And
afterwards open it in Excel. By default a file named “A” is saved on
MyDocuments folder. But if you have any trouble on open it please let me now directly to my
e-mail. Anyway, I’m sure Dr. Thimbault will soon confirm this information.</span></p>
<p class="MsoNormal"><span lang="EN-US"><br></span></p><p class="MsoNormal"><span lang="EN-US">Hoping to be
helpful,</span></p>
<p class="MsoNormal"><span lang="EN-US">M.</span></p>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-06-14 11:00 GMT+01:00 <span dir="ltr"><<a href="mailto:adegenet-forum-request@lists.r-forge.r-project.org" target="_blank">adegenet-forum-request@lists.r-forge.r-project.org</a>></span>:<div>
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Today's Topics:<br>
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1. DAPC: loadings of original variables as table? (Patricia Salerno)<br>
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<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 13 Jun 2014 16:27:10 -0500<br>
From: Patricia Salerno <<a href="mailto:patriciasalerno@gmail.com" target="_blank">patriciasalerno@gmail.com</a>><br>
To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge.r-project.org</a><br>
Subject: [adegenet-forum] DAPC: loadings of original variables as<br>
table?<br>
Message-ID:<br>
<CAHKShSk7zN-6-o35eTHGJ=fE_JVGQMQSxhbKDh=<a href="mailto:531Ejp3VQEw@mail.gmail.com" target="_blank">531Ejp3VQEw@mail.gmail.com</a>><br>
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<br>
Hi everyone,<br>
<br>
I'm using PCA/DAPC as well as STRUCTURE with a SNP matrix. I'm getting<br>
different results with the two approaches, and the DAPC results are much<br>
more logical, biologically speaking (some individuals of a very<br>
well-supported cluster in DAPC are being assigned to the other cluster,<br>
even though the separation in PC1 is enormous!). Thus, I want to see if the<br>
discrepancies of population assignment in STRUCTURE are due to the fact<br>
that the DAPC initially transforms the data into vectors that maximize<br>
variation, thus effectively weighing my variables differently, while<br>
STRUCTURE weighs all SNPs equally. The only strategy I've come up with to<br>
investigate this issue further is to generate a table of the loadings of<br>
the SNP variables (the original, not the transformed variables after PCA),<br>
and prune my matrix to only keep the SNPs with sufficient contributions<br>
(setting some post-hoc cutoff). However, I cannot figure out how to print a<br>
table of the SNP loadings after the DAPC, or if it's even possible. What I<br>
would want is a printed matrix of two columns, one with the SNP names, and<br>
another with the contributions/loadings. Could anyone help me with this?<br>
Or, does anyone have another suggestion for approaching this issue?<br>
<br>
Thank you!!<br>
<br>
~patricia.<br>
<br>
<br>
--<br>
Patricia Salerno<br>
PhD Candidate<br>
Ecology Evolution and Behavior<br>
Section of Integrative Biology<br>
University of Texas at Austin<br>
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