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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Carlo,
<br>
<br>
if you want to be conservative, you can apply Bonferroni correction to your data.
<br>
Here's an example using nancycats:<br>
<br>
> library(adegenet)<br>
> library(pegas)<br>
> temp <- hw.test(nancycats)<br>
<br>
> pval <- temp[,3]<br>
> pval<br>
fca8 fca23 fca43 fca45 fca77 fca78 <br>
0.000000e+00 0.000000e+00 0.000000e+00 1.622163e-03 0.000000e+00 0.000000e+00 <br>
fca90 fca96 fca37 <br>
0.000000e+00 1.965095e-14 1.209777e-10 <br>
<br>
> loc.to.keep <- pval < (0.05/nLoc(nancycats)) # use Bonferroni<br>
> loc.to.keep<br>
fca8 fca23 fca43 fca45 fca77 fca78 fca90 fca96 fca37 <br>
TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE <br>
> x <- nancycats[loc=loc.to.keep]<br>
<br>
<br>
Here all the loci are kept, but loci at HWE would have been filtered out.<br>
<br>
Cheers<br>
Thibaut<br>
<br>
<br>
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<div class="PlainText"> <br>
==============================<br>
Dr Thibaut Jombart<br>
MRC Centre for Outbreak Analysis and Modelling<br>
Department of Infectious Disease Epidemiology<br>
Imperial College - School of Public Health<br>
Norfolk Place, London W2 1PG, UK<br>
Tel. : 0044 (0)20 7594 3658<br>
http://sites.google.com/site/thibautjombart/<br>
http://sites.google.com/site/therepiproject/<br>
http://adegenet.r-forge.r-project.org/<br>
Twitter: @thibautjombart<br>
<br>
<br>
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<div style="direction: ltr;" id="divRpF578562"><font face="Tahoma" color="#000000" size="2"><b>From:</b> adegenet-forum-bounces@lists.r-forge.r-project.org [adegenet-forum-bounces@lists.r-forge.r-project.org] on behalf of Carlo Pecoraro [carlo.pecoraro2@unibo.it]<br>
<b>Sent:</b> 17 August 2015 16:58<br>
<b>To:</b> adegenet-forum@lists.r-forge.r-project.org<br>
<b>Cc:</b> Thibaut Jombart<br>
<b>Subject:</b> [adegenet-forum] I: HWE<br>
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<p class="MsoNormal">Hi all,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"><span lang="EN-US">I am trying to remove from my dataset those loci in HWE. I have measured it both per population: hwe.pop<-(lapply(seppop(x), hw.test) and per locus hwe.loc<-hw.test(x), B=1000).</span></p>
<p class="MsoNormal"><span lang="EN-US">Now I would like to define a threshold (0.05) for the Pr(chi^2>), removing all those loci with a derived P-values above this threshold. How could I perform this analysis? Do you have any suggestion?</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">I am wondering if this is the best way to filter my dataset according to the HWE. Any advise would be more than welcome.</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">Best regards,</span></p>
<p class="MsoNormal"><span lang="EN-US">Carlo</span></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt; font-family:"Segoe UI","sans-serif"">Da:</span></b><span style="font-size:10.0pt; font-family:"Segoe UI","sans-serif""> Carlo Pecoraro
<br>
<b>Inviato:</b> lunedì 17 agosto 2015 16:14<br>
<b>A:</b> 'adegenet-forum@lists.r-forge.r-project.org'<br>
<b>Oggetto:</b> HWE</span></p>
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<p class="MsoNormal"> </p>
<p class="MsoNormal">Hi all,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"><span lang="EN-US">I am trying to remove from my dataset those loci in HWE. I have measured it both per population: hwe.pop<-(lapply(seppop(x), hw.test) and per locus hwe.loc<-hw.test(x), B=1000).</span></p>
<p class="MsoNormal"><span lang="EN-US">Now I would like to define a threshold (0.05) for the Pr(chi^2>), removing all those loci with a derived P-values above this threshold. How could I perform this analysis? Do you have any suggestion?</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">I am wondering if this is the best way to filter my dataset according to the HWE. Any advise would be more than welcome.</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">Best regards,</span></p>
<p class="MsoNormal"><span lang="EN-US">Carlo</span></p>
<p class="MsoNormal" style="background:white"><b><span style="font-size:12.0pt; font-family:"Cambria","serif"; color:#1F497D; background:white" lang="EN-US">--</span></b></p>
<p class="MsoNormal" style="background:white"><b><span style="font-size:12.0pt; font-family:"Cambria","serif"; color:#1F497D; background:white" lang="EN-US"> </span></b></p>
<p class="MsoNormal" style="background:white"><b><span style="font-size:12.0pt; font-family:"Cambria","serif"; color:#1F497D; background:white" lang="EN-US">Carlo Pecoraro, PhD Candidate</span></b><span style="font-size:13.5pt; font-family:"Segoe UI","sans-serif"; color:black" lang="EN-US"></span></p>
<p class="MsoNormal" style="background:white"><b><span style="font-size:12.0pt; font-family:"Cambria","serif"; color:#1F497D; background:white" lang="EN-US"><br>
</span></b><i><span style="font-size:10.0pt; color:#1F497D; background:white" lang="EN-US">Laboratory of Genetics & Genomics of Marine Resources and Environment (GenoDREAM)<br>
Dept.</span></i><i><span style="font-size:10.0pt; color:#1F497D" lang="EN-US"> <span style="background:white">Biological, Geological & Environmental Sciences (BiGeA)<br>
University of Bologna<br>
Via S. Alberto 163, 48123 Ravenna (Italy)</span></span></i></p>
<p class="MsoNormal" style="background:white"><i><span style="font-size:10.0pt; color:#1F497D; background:white" lang="EN-US"> </span></i></p>
<p class="MsoNormal" style="background:white"><i><span style="font-size:10.0pt; color:#1F497D" lang="EN-US">IRD (Institut de Recherche pour le Développement)<br>
UMR 212 EME (Ecosytèmes Marins Exploités)<br>
BP 570<br>
Victoria, Mahé<br>
Seychelles</span></i></p>
<p class="MsoNormal" style="background:white"><i><span style="font-size:10.0pt; color:#1F497D; background:white" lang="EN-US"><br>
</span></i><i><span style="font-size:10.0pt; color:#1F497D; background:white">Ph: +39 3337603101</span></i><i><span style="font-size:10.0pt; color:#1F497D"></span></i></p>
<p class="MsoNormal" style="background:white"><i><span style="font-size:10.0pt; color:#1F497D; background:white">skype contact: carlo_pecoraro</span></i><i><span style="font-size:10.0pt; color:#1F497D"></span></i></p>
<p class="MsoNormal"> </p>
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