<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">Hi Jeremy,</div><div class=""><br class=""></div><div class=""><blockquote type="cite" class="">I'm wondering if this the right way (statistically speaking) to analyse mixed ploidy datasets in R? Will my estimates of genetic diversity and structure be accurate?</blockquote><div class=""><br class=""></div><div class="">I think the answer is... it depends. Meirmans, Liu, and Tienderen just came out with a review on this topic: <a href="https://doi.org/10.1093/jhered/esy006" class="">https://doi.org/10.1093/jhered/esy006</a>*. For multivariate analyses (sPCA, PCA, DAPC, etc), you will want to reduce the effect of polyploidy by converting your data to allele frequencies with:</div><div class=""><br class=""></div><div class="">tab(myData, freq = TRUE)</div><div class=""><br class=""></div><div class="">If you have an organism that changes ploidy by life stage, you may need to analyze them separately. Moreover, if you use Bruvo's distance, the choice of model is very important. </div><div class=""><br class=""></div><blockquote type="cite" class="">I know there is the POLYSAT package, which seems to have been developed specifically for dealing with mixed ploidy datasets, however, I would rather stick to using adagenet and poppr, as I'm familiar with the functions and the structure of genind and genclone objects.</blockquote><br class=""></div><div class="">I know conversion is a PITA, but I would highly recommend using POLYSAT. There are far more tools to deal with polyploidy in that package that can complement any analyses you would perform with poppr or adegenet. A few years ago, I wrote a tiny function to help with conversion from genind to polysat data:</div><div class=""><br class=""></div><div class=""><a href="https://gist.github.com/zkamvar/aeaff83b9d126d55aade" class="">https://gist.github.com/zkamvar/aeaff83b9d126d55aade</a></div><div class=""><br class=""></div><div class="">In fact, Clarke and Schreier came out with a paper a year ago talking about how to resolve ambiguous ploidy, and it's only available in polysat: <a href="http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12639/abstract" class="">http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12639/abstract</a> </div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Hope that helps,</div><div class="">Zhian</div><div class=""><br class=""></div><div class="">* The last figure in this paper will change slightly since they used an old version of poppr to calculate Bruvo's distance, which had a silent bug. </div><br class=""><div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">-----</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">Zhian N. Kamvar, Ph. D.</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">Postdoctoral Researcher (Everhart Lab)</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">Department of Plant Pathology</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">University of Nebraska-Lincoln</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">ORCID: 0000-0003-1458-7108</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br class=""></div><br class="Apple-interchange-newline"></div></div><div><blockquote type="cite" class=""><div class=""><div class=""><br class="">Date: Fri, 9 Feb 2018 00:48:39 +0000<br class="">From: JEREMY SAMUEL BENWELL-CLARKE <<a href="mailto:17197751@students.latrobe.edu.au" class="">17197751@students.latrobe.edu.au</a>><br class="">To: "<a href="mailto:adegenet-forum@lists.r-forge.r-project.org" class="">adegenet-forum@lists.r-forge.r-project.org</a>"<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><<a href="mailto:adegenet-forum@lists.r-forge.r-project.org" class="">adegenet-forum@lists.r-forge.r-project.org</a>><br class="">Subject: [adegenet-forum] Analysing mixed ploidy datasets<br class="">Message-ID:<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><<a href="mailto:SY3PR01MB15646BCB509043E46D83877FC7F20@SY3PR01MB1564.ausprd01.prod.outlook.com" class="">SY3PR01MB15646BCB509043E46D83877FC7F20@SY3PR01MB1564.ausprd01.prod.outlook.com</a>><br class=""><span class="Apple-tab-span" style="white-space:pre"> </span><br class="">Content-Type: text/plain; charset="us-ascii"<br class=""><br class="">Hi everyone,<br class=""><br class="">I'm trying to analyse a mixed ploidy dataset. The majority of my samples are diploid but there are a few triploids too. To make ploidy even in my raw data matrix I added zeros to all my diploid samples, which makes them triploids. I then use the read.genalex function from the poppr package to read in my data setting ploidy=3. However, I don't want '0' to be recognised as an extra allele and I want the true diploid samples to be separate from the true triploid samples. Therefore, I use the recode_polyploids function from poppr and set newploidy=T. Here is my code:<br class=""><br class="">genclone<-read.genalex("C:/Users/...", ploidy = 3)<br class="">genclone<-recode_polyploids(genclone, newploidy = T)<br class=""><br class=""><br class="">I'm wondering if this the right way (statistically speaking) to analyse mixed ploidy datasets in R? Will my estimates of genetic diversity and structure be accurate?<br class="">I know there is the POLYSAT package, which seems to have been developed specifically for dealing with mixed ploidy datasets, however, I would rather stick to using adagenet and poppr, as I'm familiar with the functions and the structure of genind and genclone objects.<br class=""><br class="">Any help would be much appreciated!<br class=""><br class="">Cheers,<br class=""><br class="">Jeremy<br class="">-------------- next part --------------<br class="">An HTML attachment was scrubbed...<br class="">URL: <<a href="http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20180209/7c415c08/attachment-0001.html" class="">http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20180209/7c415c08/attachment-0001.html</a>><br class=""><br class="">------------------------------<br class=""><br class="">_______________________________________________<br class="">adegenet-forum mailing list<br class=""><a href="mailto:adegenet-forum@lists.r-forge.r-project.org" class="">adegenet-forum@lists.r-forge.r-project.org</a><br class="">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum<br class=""><br class="">End of adegenet-forum Digest, Vol 114, Issue 7<br class="">**********************************************<br class=""></div></div></blockquote></div><br class=""></body></html>