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<p class="MsoNormal">Hi Brian,</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you for the help. I was avoiding to subset my data because I am interested in investigating SNPs that could be related to a change in morph between these populations.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Cheers,</p>
<p class="MsoNormal">Rachel</p>
<p class="MsoNormal"><o:p> </o:p></p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> brian knaus <briank.lists@gmail.com><br>
<b>Sent:</b> Tuesday, March 5, 2019 2:05:03 PM<br>
<b>To:</b> Rachel Turba<br>
<b>Cc:</b> adegenet-forum@lists.r-forge.r-project.org<br>
<b>Subject:</b> Re: [adegenet-forum] Scripting adegenet with whole-genome data</font>
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<div>Hi Rachel,</div>
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<div>Demographic patterns are generally thought to occur throughout the genome. In which case you shouldn't need the entire genome but can use a representative subset of your variants. We've demonstrated how to accomplish this at the below link.</div>
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<div><a href="https://grunwaldlab.github.io/Population_Genetics_in_R/gbs_analysis.html#subsetting-a-vcfr-object-to-200-random-variants">https://grunwaldlab.github.io/Population_Genetics_in_R/gbs_analysis.html#subsetting-a-vcfr-object-to-200-random-variants</a><br>
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<div>Good luck!</div>
<div>Brian<br>
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<div dir="ltr" class="gmail_attr">On Tue, Mar 5, 2019 at 11:24 AM Rachel Turba <<a href="mailto:rturba@outlook.com">rturba@outlook.com</a>> wrote:<br>
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<p class="MsoNormal">Hi all,</p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I have researched this on the forum but was not successful in finding help, so I apologize in advance if this has been addressed already.</p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">In this tutorial (<a href="https://grunwaldlab.github.io/Population_Genetics_in_R/DAPC.html" target="_blank">https://grunwaldlab.github.io/Population_Genetics_in_R/DAPC.html</a>) it says that adegenet cannot be scripted a priori, but my
data has 6Gb and takes a very long time to generate the DAPC object. So I have to submit it as a script to the university cluster. I get the plot of variance explained by PC but then everything halts because I do not provide the number of PCs to be retained
for continuing the analysis. Is there a way around this? How does anyone handle large datasets?</p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thank you in advance,</p>
<p class="MsoNormal">Rachel</p>
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