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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi Angela,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">I’ve done something similar with a data set for ~900,000 SNPs where I only had allele frequencies per each of my ‘populations’. I simply
imported this as a matrix where each value was the ‘A’ allele frequency and did my dapc etc from there. Not sure if this will work well given the much larger number of SNPs you have but worth a try.
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Mark<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> adegenet-forum-bounces@lists.r-forge.r-project.org [mailto:adegenet-forum-bounces@lists.r-forge.r-project.org]
<b>On Behalf Of </b>Angela Fuentes Pardo<br>
<b>Sent:</b> 30 October 2017 15:24<br>
<b>To:</b> adegenet-forum@lists.r-forge.r-project.org<br>
<b>Subject:</b> [adegenet-forum] Could adegenet be modified to accept allele frequencies as input data?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">Hi there,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">My dataset consists of allele frequencies of millions of SNPs for >10 populations (I don't have individual genotype data). adegenet requires individual genotypes as input data,
but considering many population genetic tests are based on allele frequencies, I wanted to ask if there is any possibility that adegenet could have a function that accepts population allele frequencies as input data. I am mostly interested on conducting PCA
and DAPC tests.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">Thanks<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black">--<b><br>
Angela P. Fuentes-Pardo</b>. Biologist, Ph.D. candidate<span style="letter-spacing:-.25pt"><br>
Ruzzante Lab, Department of Biology</span><br>
Dalhousie University<span style="letter-spacing:-.25pt">, Halifax, Canada, B3H 4R2<br>
<a href="http://fuentespardo.weebly.com" id="LPNoLP"><span style="color:black">http://fuentespardo.weebly.com</span></a><br>
<br>
</span></span><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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Inverness College UHI, a partner in the University of the Highlands and Islands www.inverness.uhi.ac.uk Board of Management of Inverness College (known as Inverness College UHI), Scottish Charity No SC021197.
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