<p dir="ltr">Hi there, <br>
Please check carefully the error msg. Here the problem is stated clearly. You either need to provide the group factor as argument to dapc, or to attach it to the object - pop(x) <- ... </p>
<p dir="ltr">Cheers<br>
Thibaut</p>
<div class="gmail_extra"><br><div class="gmail_quote">On 2 Sep 2016 09:51, "Bhuller, Ravneet" <<a href="mailto:ravneet.bhuller13@imperial.ac.uk">ravneet.bhuller13@imperial.ac.uk</a>> wrote:<br type="attribution"><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
Hello Thibaut,
<div>
<div><br>
</div>
<div>The genind object is of size 8.9 Mb.</div>
<div><br>
</div>
<div>Yesterday, when I tried find.clusters in the Rmarkdown document, it did not ask for any input. I wanted to know how many components to retain to run DAPC.</div>
<div><br>
</div>
<div>However, today, when I tried find.clusters in R (without Rmarkdown), it worked absolutely fine.</div>
<div><br>
</div>
<div>But another problem is that pop function is giving an error. Attached is the screenshot. My data is DNA multiple-sequence-alignment FASTA files of 357 genes, which are concatenated. Each file has same 220 bacterial strains. And my meta data includes
220 strains distributed into 19 serovars (integers). Is my meta data in the correct required form?</div>
<div><br>
</div>
<div><img height="200" width="320" src="cid:943D7881-6E60-444E-8038-5754883AF5B2@dlink.com"></div>
<div><br>
</div>
<div>Kind regards,</div>
<div><br>
</div>
<div>Rav</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div>
<blockquote type="cite"><div class="quoted-text">
<div>On 1 Sep 2016, at 16:17, Thibaut Jombart <<a href="mailto:thibautjombart@gmail.com" target="_blank">thibautjombart@gmail.com</a>> wrote:</div>
<br>
</div><div><div class="quoted-text">Hi,<br>
<br>
what is the size of the dataset? Are you sure it did not display a graph of<br>
cumulative variance and waits for your input? As you specified it, the<br>
function is interactive and will wait on your input before giving results.<br>
<br>
Best<br>
Thibaut<br>
<br>
<br>
--<br>
Dr Thibaut Jombart<br>
Lecturer, Department of Infectious Disease Epidemiology<br>
Imperial College London<br>
<a href="https://sites.google.com/site/thibautjombart/" target="_blank">https://sites.google.com/site/<wbr>thibautjombart/</a><br>
<a href="https://github.com/thibautjombart" target="_blank">https://github.com/<wbr>thibautjombart</a><br></div>
Twitter: @TeebzR <<a href="https://twitter.com/TeebzR" target="_blank">https://twitter.com/TeebzR</a>><div class="elided-text"><br>
<br>
On 1 September 2016 at 00:33, Graham Reynolds <<a href="mailto:greynold@unca.edu" target="_blank">greynold@unca.edu</a>> wrote:<br>
<br>
<blockquote type="cite">Hi Rav, if you have multiple cores on your CPU you can distribute the task<br>
among them, which really speeds it up. That might at least let you see<br>
whether it is a problem with the dataset.<br>
<br>
grp <-find.clusters(app, max.n.clust=n, parallel = "multicore", ncpus = 4)<br>
<br>
You might need to install the Parallel package<br>
<br>
Cheers<br>
<br>
<br>
R. Graham Reynolds, Ph.D.<br>
Assistant Professor of Biology<br>
University of North Carolina Asheville<br>
<a href="http://www.caribbeanboas.org" target="_blank">www.caribbeanboas.org</a><br>
<br>
<br>
<br>
*From:* R-sig-genetics <<a href="mailto:r-sig-genetics-bounces@r-project.org" target="_blank">r-sig-genetics-bounces@r-<wbr>project.org</a>> on behalf of<br>
Bhuller, Ravneet <<a href="mailto:ravneet.bhuller13@imperial.ac.uk" target="_blank">ravneet.bhuller13@imperial.<wbr>ac.uk</a>><br>
<br>
<blockquote type="cite">*Sent:* Wednesday, August 31, 2016 5:39 AM<br>
*To:* <a href="mailto:r-sig-genetics@r-project.org" target="_blank">r-sig-genetics@r-project.org</a><br>
*Subject:* [R-sig-genetics] Query regarding DAPC using ADEGENT in R<br>
<br>
Dear All,<br>
<br>
I am trying to do DAPC on my genind object (app) using ADEGENET in R. But<br>
when I run the following command:<br>
<br>
grp <- find.clusters(app)<br>
<br>
it is processing continuously for more than 2 hours but not producing any<br>
output. Any guidance will be very much appreciated.<br>
<br>
Regards,<br>
<br>
Rav<br>
<br>
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