<div dir="ltr">Hi Flo, <div><br></div><div>sorry about the late reply. I'd make an excuse, but it won't bit "been busy". In short:</div><div><br></div><div>There is no proper solution to the group labelling issue you mention, at least none that I know if. A workaround I have used alongside other colleagues uses two statistics, relying on all pairwise comparisons of individuals in the clusters:</div><div>- % of times 2 indiv are in the same cluster when they should</div><div>- % of times 2 indiv are in different clusters when they should</div><div><br></div><div>The average of the two quantities is I think the rand index:</div><div><a href="https://en.wikipedia.org/wiki/Rand_index">https://en.wikipedia.org/wiki/Rand_index</a><br></div><div><br></div><div>For the second, simple answer: DAPC is *bad* at finding hybrids. For this, consider using the soon-to-be-published (hopefully) method 'snapclust', also in adegenet. Doc for this is hidden there:</div><div><a href="https://github.com/thibautjombart/adegenet/raw/master/tutorials/tutorial-snapclust.pdf">https://github.com/thibautjombart/adegenet/raw/master/tutorials/tutorial-snapclust.pdf</a><br></div><div><br></div><div>Best<br></div><div>Thibaut</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><br>--<br>Dr Thibaut Jombart<br>Lecturer, Department of Infectious Disease Epidemiology, Imperial College London<br>Head of RECON: <a href="http://repidemicsconsortium.org" target="_blank">repidemicsconsortium.org</a><br>WHO Consultant - outbreak analysis<br><a href="http://sites.google.com/site/thibautjombart/" target="_blank">sites.google.com/site/thibautjombart/</a><br>Twitter: @TeebzR<br>+44(0)20 7594 3658</div></div>
<br><div class="gmail_quote">On 21 November 2017 at 18:45, Florian Leplat <span dir="ltr"><<a href="mailto:leplat.florian@gmail.com" target="_blank">leplat.florian@gmail.com</a>></span> wrote:<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">Dear Adegenet user,</span></p><p class="MsoNormal"><span lang="EN-US"><br></span></p><p class="MsoNormal"><span lang="EN-US">I was
previously using adegenet package for genetic applications.</span></p>
<p class="MsoNormal"><span lang="EN-US">Since I
started to use the DAPC function. The methods is very informative. However
there are some details that I would like to understand better.</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">The main
objective of my use is to group a certain number of plant genotype regarding to
their genotypic background.</span><span lang="EN-US"> Each
genotype are homozygous lines.</span>
</p><p class="MsoNormal"><span lang="EN-US">I have no
prerequisite information for any genotype. Therefore the main idea is to
attribute a “group number” for each of my plants.</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">I does work
fine with a good comprehensiveness regarding to the information that I have
for each plants (origin, parents...)<br></span></p>
<p class="MsoNormal"><span lang="EN-US">However,
one of the limitations that I face is the repeatability of the grouping. If
running several time, a certain number of plant will be attributed to a
different group. Is there a cross-validation procedure at this step in order to
look at the percentage of plant always grouped together for each run ?</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">Furthermore,
even if my grouping are quite consistent “group wise” from one run to the
other, the grouping number will change. Is there a way to solve that (for
instance give a group number to the founder genotype of our population) ?</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">Then I have
a second issue. After the first step which define my groups, I would like to
plot hybrids genotypes which should (could) be an admixture between 2 groups. Therefore
I cannot use them to build my groups as they add some noise to the model. I
wanted to use the procedure described in the tutorial using supplementary
individuals. I realized that it only works if the supplementary individuals
have already grouping information, however I don’t have this information.
Indeed I only want to see (mostly visually) where the hybrids are positioned in
relation to the other groups that I previously defined. Is there a way to use
the script to do that ?</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">Thanks in
advance for your help.</span></p>
<p class="MsoNormal"><span lang="EN-US">Best
regards.</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<div class="m_-6086506409520949012gmail_signature"><div dir="ltr"><div><div><b>Flo</b><span></span></div></div></div></div>
</div>
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