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<p class="MsoNormal"><a name="_MailEndCompose"><span style="color:#1F497D">Hi Thibaut,<o:p></o:p></span></a></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">many thanks once again...<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Cheers<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Carlo<o:p></o:p></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""> Jombart, Thibaut [mailto:t.jombart@imperial.ac.uk]
<br>
<b>Inviato:</b> giovedì 20 agosto 2015 18:05<br>
<b>A:</b> Carlo Pecoraro; adegenet-forum@lists.r-forge.r-project.org<br>
<b>Oggetto:</b> RE: HWE<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt;
font-family:"Tahoma","sans-serif";color:black">Hi Carlo,
<br>
<br>
I am confused - I thought you wanted to keep only loci *not* in HWE? <br>
<br>
Yes, what you describe is doable - only a bit more cumbersome. You need to use seppop and then sapply over the objects:<br>
<br>
data(nancycats)<br>
hw.test(nancycats)<br>
allPval <- sapply(seppop(nancycats), function(e) hw.test(e, B=0)[,3,drop=FALSE])<br>
<br>
and allPval contains the pvalues for all loci (row) and populations (columns).<br>
>From that it's trivial to get what you need, e.g.<br>
apply(allPval<0.05, 1, sum, na.rm=TRUE) > 8<br>
<br>
To get the loci with significant departure from HWE in at least 8 populations (just tweak the 0.05 to use correction for multiple testing).<br>
<br>
Cheers<br>
Thibaut<br>
<br>
<br>
<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:10.0pt;
font-family:"Tahoma","sans-serif";color:black">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> Carlo Pecoraro [carlo.pecoraro2@unibo.it]<br>
<b>Sent:</b> 18 August 2015 12:42<br>
<b>To:</b> Jombart, Thibaut<br>
<b>Subject:</b> R: HWE</span><span style="font-size:12.0pt;font-family:"Times New Roman","serif";
color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#1F497D">Hi Thibaut,</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">first of all many thanks for your answer.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">It works perfectly..many thanks for that!</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">The problem is that in this way I am going to lose more than 1000 loci in my dataset.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">I am wondering if I have just to remove those loci which are out of Hardy–Weinberg equilibrium in at least the 80/90% of my geographical samples/populations (i.e. 8/10).
</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Would it be possible to filter out those loci in disequilibrium, for instance, in 8 o more populations?</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Sorry for disturbing you again with these boring stuff.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Many thanks for your help.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Cheers,</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D">Carlo</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Segoe UI","sans-serif";
color:black">Da:</span></b><span style="font-size:10.0pt;font-family:"Segoe UI","sans-serif";
color:black"> Jombart, Thibaut [mailto:t.jombart@imperial.ac.uk]
<br>
<b>Inviato:</b> lunedì 17 agosto 2015 18:16<br>
<b>A:</b> Carlo Pecoraro; adegenet-forum@lists.r-forge.r-project.org<br>
<b>Oggetto:</b> RE: HWE</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt;
font-family:"Tahoma","sans-serif";color:black">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</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.0pt;
font-family:"Tahoma","sans-serif";color:black">
<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</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:10.0pt;
font-family:"Tahoma","sans-serif";color:black">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> 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</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Hi all,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">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><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">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><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">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><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">Best regards,</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">Carlo</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Segoe UI","sans-serif";
color:black">Da:</span></b><span style="font-size:10.0pt;font-family:"Segoe UI","sans-serif";
color:black"> 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><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Hi all,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">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><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">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><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">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><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">Best regards,</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">Carlo</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><b><span lang="EN-US" style="font-size:12.0pt;font-family:"Cambria","serif";color:#1F497D;background:
white">--</span></b><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><b><span lang="EN-US" style="font-size:12.0pt;font-family:"Cambria","serif";color:#1F497D;background:
white"> </span></b><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><b><span lang="EN-US" style="font-size:12.0pt;font-family:"Cambria","serif";color:#1F497D;background:
white">Carlo Pecoraro, PhD Candidate</span></b><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><b><span lang="EN-US" style="font-size:12.0pt;font-family:"Cambria","serif";color:#1F497D;background:
white"><br>
</span></b><i><span lang="EN-US" style="font-size:10.0pt;color:#1F497D;
background:white">Laboratory of Genetics & Genomics of Marine Resources and Environment (GenoDREAM)<br>
Dept.</span></i><i><span lang="EN-US" style="font-size:10.0pt;color:#1F497D"> <span style="background:white">Biological, Geological & Environmental Sciences (BiGeA)<br>
University of Bologna<br>
Via S. Alberto 163, 48123 Ravenna (Italy)</span></span></i><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><i><span lang="EN-US" style="font-size:10.0pt;color:#1F497D;background:white"> </span></i><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><i><span lang="EN-US" style="font-size:10.0pt;color:#1F497D">IRD (Institut de Recherche pour le Développement)<br>
UMR 212 EME (Ecosytèmes Marins Exploités)<br>
BP 570<br>
Victoria, Mahé<br>
Seychelles</span></i><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><i><span lang="EN-US" style="font-size:10.0pt;color:#1F497D;background:white"><br>
</span></i><i><span style="font-size:10.0pt;color:#1F497D;background:white">Ph: +39 3337603101</span></i><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><i><span style="font-size:10.0pt;
color:#1F497D;background:white">skype contact: carlo_pecoraro</span></i><span style="color:black"><o:p></o:p></span></p>
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