<html><body><div style="font-family: trebuchet ms,sans-serif; font-size: 12pt; color: #000000"><div>It goes without saying that order in your vcf (pops_list) file should correspond to the order in your datapop.</div><div><br data-mce-bogus="1"></div><div>To assign population to your pops_list should be a vector or a factor like so:</div><div><br data-mce-bogus="1"></div><div>library(adegenet)<br>data(nancycats)<br>pop(nancycats) <- 1:237<br></div><div><br data-mce-bogus="1"></div><div>(see basics manual at https://github.com/thibautjombart/adegenet/wiki/Tutorials)</div><div><br data-mce-bogus="1"></div><div>If you want to assign names to your populations, you can use popNames(x) <- y.</div><div><br data-mce-bogus="1"></div><div>Cheers,</div><div>Roman</div><div><br></div><div data-marker="__SIG_PRE__">----<br>In god we trust, all others bring data.<br>> Zahtevaj IJZ na https://kurc.biolitika.si</div><br><hr id="zwchr" data-marker="__DIVIDER__"><div data-marker="__HEADERS__"><b>From: </b>"Didier Aurelle" <aurelle.didier@gmail.com><br><b>To: </b>adegenet-forum@lists.r-forge.r-project.org<br><b>Sent: </b>Wednesday, October 11, 2017 12:08:05 PM<br><b>Subject: </b>[adegenet-forum] define population level for PCA analysis in adegenet<br></div><br><div data-marker="__QUOTED_TEXT__"><div dir="ltr">Dear all<br><br><div class="gmail-post-text">
<p>I want to perform a PCA analysis in adegenet starting from a genepop file without defined populations.
I imported the data like this:
datapop <- read.genepop('tous.gen', ncode=3, quiet = FALSE)</p>
<p>it works, and I can perform a PCA after scaling the data.
But I would like to plot the results / individuals on the PCA axis
according to their population of origin using s.class. I have a vcf file
with a three lettre code for each individual. I imported it in R:
pops_list <- read.csv('liste_pops.csv', header=FALSE)</p>
<p>but now how can I use it to define population levels in the genind object 'datapop'?
I tried something likes this:
setPop(datapop, formula = NULL)</p>
<p>setPop(datapop) <- pops_list
but it doesn't work; even the first line doesn't work: I get this message: "Erreur : formula must be a valid formula object."</p>
<p>And then how should I use it in s.class? <br></p><p>thanks</p><p>Didier</p>
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