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<p class="MsoNormal">Hi Brian</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Yes, I think I will have to try that. I am not sure either if it will work but in the tutorial there was a step that looked at SNPs contributing to the variation in the set. I just thought it would be worth trying as an alternative tool
alongside genome wide Fst.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you so much for the advice and help.</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> Wednesday, March 6, 2019 1:27:02 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>
<div><br>
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<div>I believe that the statement for why DAPC can not be scripted is because the steps to determine the number of principal components and discriminant functions are interactive. If you know this information you can send the DAPC step to a server without a
monitor. Not sure DAPC is going to help you find SNPs associated with phenotypes though.</div>
<div><br>
</div>
<div>Good luck!</div>
<div>Brian<br>
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<br>
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<div dir="ltr" class="gmail_attr">On Wed, Mar 6, 2019 at 11:14 AM Rachel Turba <<a href="mailto:rturba@outlook.com">rturba@outlook.com</a>> wrote:<br>
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<p class="MsoNormal">Hi Brian,</p>
<p class="MsoNormal"><u></u> <u></u></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"><u></u> <u></u></p>
<p class="MsoNormal">Cheers,</p>
<p class="MsoNormal">Rachel</p>
<p class="MsoNormal"><u></u> <u></u></p>
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<div id="gmail-m_-7965030034425534424divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> brian knaus <<a href="mailto:briank.lists@gmail.com" target="_blank">briank.lists@gmail.com</a>><br>
<b>Sent:</b> Tuesday, March 5, 2019 2:05:03 PM<br>
<b>To:</b> Rachel Turba<br>
<b>Cc:</b> <a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">
adegenet-forum@lists.r-forge.r-project.org</a><br>
<b>Subject:</b> Re: [adegenet-forum] Scripting adegenet with whole-genome data</font>
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<div>Hi Rachel,</div>
<div><br>
</div>
<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>
<div><br>
</div>
<div><a href="https://grunwaldlab.github.io/Population_Genetics_in_R/gbs_analysis.html#subsetting-a-vcfr-object-to-200-random-variants" target="_blank">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><br>
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<div>Good luck!</div>
<div>Brian<br>
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<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Mar 5, 2019 at 11:24 AM Rachel Turba <<a href="mailto:rturba@outlook.com" target="_blank">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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