<div dir="ltr">Hi Marta, <div><br></div><div>the function find.clusters has methods for matrix and data.frame objects. Easiest way to proceed is use 'tab' to extract allele frequencies from your genind object and replace missing values, and then use find.clusters on it. </div><div><br></div><div>For instance:</div><div><font face="monospace, monospace"><br></font></div><div><div><font face="monospace, monospace">> data(microbov)</font></div><div><font face="monospace, monospace">> summary(microbov)</font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">// Number of individuals: 704</font></div><div><font face="monospace, monospace">// Group sizes: 50 50 51 30 50 50 47 61 31 55 50 50 49 30 50</font></div><div><font face="monospace, monospace">// Number of alleles per locus: 9 7 12 5 11 9 7 12 13 9 13 16 14 14 14 10 10 19 11 13 17 12 16 13 12 15 8 22 21 9</font></div><div><font face="monospace, monospace">// Number of alleles per group: 251 235 143 179 194 212 146 196 176 200 213 186 191 168 188</font></div><div><font face="monospace, monospace"><b>// Percentage of missing data: 2.32 %</b></font></div><div><font face="monospace, monospace">// Observed heterozygosity: 0.55 0.54 0.69 0.45 0.64 0.6 0.29 0.59 0.68 0.58 0.66 0.71 0.6 0.71 0.8 0.64 0.45 0.64 0.65 0.63 0.66 0.66 0.59 0.74 0.68 0.77 0.62 0.69 0.68 0.44</font></div><div><font face="monospace, monospace">// Expected heterozygosity: 0.71 0.6 0.78 0.54 0.79 0.76 0.49 0.69 0.83 0.77 0.77 0.82 0.75 0.76 0.89 0.75 0.63 0.77 0.75 0.78 0.77 0.77 0.77 0.84 0.74 0.89 0.69 0.77 0.89 0.56</font></div><div><font face="monospace, monospace"><br></font></div></div><div><div><font face="monospace, monospace">> x <- tab(microbov, freq=TRUE, <b>NA.method="mean"</b>) # replace missing values here</font></div><div><font face="monospace, monospace">> g <- find.clusters(x)</font></div><div><font face="monospace, monospace">Choose the number PCs to retain (>=1): </font></div></div><div><font face="monospace, monospace">....</font></div><div><br></div><div>Best</div><div>Thibaut</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div><div><br>--<br>Dr Thibaut Jombart<br>Lecturer, Department of Infectious Disease Epidemiology<br></div></div>Imperial College London<br><a href="https://sites.google.com/site/thibautjombart/" target="_blank">https://sites.google.com/site/thibautjombart/</a><br></div><div><a href="https://github.com/thibautjombart" target="_blank">https://github.com/thibautjombart<br></a></div>Twitter: <a href="https://twitter.com/TeebzR" target="_blank">@TeebzR</a><br></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On 1 August 2016 at 14:18, Marta Piotrowska <span dir="ltr"><<a href="mailto:Marta.Piotrowska@sruc.ac.uk" target="_blank">Marta.Piotrowska@sruc.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="EN-GB" link="blue" vlink="purple">
<div>
<p class="MsoNormal">Dear Members,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I am trying to use find.cluster function in adegenet package for my microsat data analysis but I can’t find anywhere information if it accepts missing values. I tried NAs but it seems not to like it. I know that one way around it is to
remove all the samples with missing values but I wondered if there is alternative allowing me to keep the missing values?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I will be grateful for your help.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Regards,<u></u><u></u></p>
<p class="MsoNormal">Marta<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Cambria","serif"">Marta Piotrowska, PhD.<u></u><u></u></span></i></p>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Cambria","serif"">Postdoctoral Researcher<u></u><u></u></span></i></p>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Cambria","serif"">Crop and Soil Systems Group<u></u><u></u></span></i></p>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Cambria","serif"">SRUC<u></u><u></u></span></i></p>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Cambria","serif"">West Mains Road<u></u><u></u></span></i></p>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Cambria","serif"">Edinburgh EH9 3JG<u></u><u></u></span></i></p>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Cambria","serif""><u></u> <u></u></span></i></p>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Cambria","serif"">Phone: 01315354294</span></i><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
<p class="MsoNormal"><i><span><a href="mailto:Marta.Piotrowska@sruc.ac.uk" target="_blank"><span style="color:blue">Marta.Piotrowska@sruc.ac.uk</span></a></span></i><i><span><u></u><u></u></span></i></p>
<p class="MsoNormal"><i><span><u></u> <u></u></span></i></p>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Cambria","serif""><u></u> <u></u></span></i></p>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Cambria","serif""><u></u> <u></u></span></i></p>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div><font face="Webdings" color="green" size="5"><span style="FONT-SIZE:18pt;COLOR:green;FONT-FAMILY:Webdings"><br>
</span></font><font color="#21c0ef" size="2"><span style="FONT-SIZE:10pt;COLOR:#21c0ef"></span></font><font face="Arial" color="green" size="1"><span style="FONT-SIZE:8pt;COLOR:green;FONT-FAMILY:Arial">Please don't print this e-mail unless you really
need to. </span></font></div>
<div>
<div>
<p class="MsoNormal"><font face="Arial" size="2"><span style="FONT-SIZE:10pt;FONT-FAMILY:Arial">This e-mail message is confidential to the intended recipient at the email address to which it has been addressed. If the message has been received by you in
error, it may not be disclosed to or used by anyone other than the intended addressee, nor may it be copied in any way. If it is not intended for you please inform us, immediately, then delete it from your system. If the content is not about the business of
the organisation then the message is not from us nor is it sanctioned by us. Anything in this e-mail or its attachments which does not relate to SRUC's or SAC Commercial Limited's official business is neither given nor endorsed by SRUC or SAC Commercial Limited.
</span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span style="FONT-SIZE:8pt;FONT-FAMILY:Arial">SRUC
<br>
A Charitable company limited by guarantee, Scottish Charity Number: SC003712. <br>
Registered in Scotland, Company Number: SC103046 - Registered Office: Peter Wilson Building, King’s Buildings, West Mains Road, Edinburgh EH9 3JG
<br>
SAC Commercial Limited, an SRUC company <br>
Registered in Scotland, Company Number: SC148684 - Registered Office: Peter Wilson Building, King’s Buildings, West Mains Road, Edinburgh EH9 3JG
</span></font></p>
</div>
</div>
</div>
<br>_______________________________________________<br>
adegenet-forum mailing list<br>
<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
<a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum" rel="noreferrer" target="_blank">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum</a><br></blockquote></div><br></div>