Thanks Fre for this nice email object :-) it reads like I am a locus under selection!<br><br><div class="gmail_quote">On 4 December 2012 09:00, Frederik Van den Broeck <span dir="ltr"><<a href="mailto:Frederik.VandenBroeck@bio.kuleuven.be" target="_blank">Frederik.VandenBroeck@bio.kuleuven.be</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Lositan or Bayescan are easy to use and will do the job!<br>
<br>
Fre<br>
<br>
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From: <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a> [<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>] on behalf of <a href="mailto:adegenet-forum-request@lists.r-forge.r-project.org">adegenet-forum-request@lists.r-forge.r-project.org</a> [<a href="mailto:adegenet-forum-request@lists.r-forge.r-project.org">adegenet-forum-request@lists.r-forge.r-project.org</a>]<br>
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Today's Topics:<br>
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1. detecting outliers - loci under selection (Mayte Ruiz)<br>
2. Re: detecting outliers - loci under selection (Jombart, Thibaut)<br>
3. Re: detecting outliers - loci under selection (Valeria Montano)<br>
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----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 27 Nov 2012 09:58:21 -0400<br>
From: Mayte Ruiz <<a href="mailto:mayaruizz@gmail.com">mayaruizz@gmail.com</a>><br>
To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
Subject: [adegenet-forum] detecting outliers - loci under selection<br>
Message-ID:<br>
<CABBTkLa6w1JOt_ci7aWmyuF1_C=iV6VOXRaN2P_+q=<a href="mailto:whAfZCAQ@mail.gmail.com">whAfZCAQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear Thibaut Jombart and adegenet users,<br>
<br>
I am working with RAD sequenced data of 2 populations with only 10<br>
individuals each but with many many loci. I have been searching for a<br>
program which detects outliers (loci under selection) from my data. A<br>
colleague has suggested adegenet as a possibility. Can adegenet be used<br>
for this? I have searched the manual but do not yet find anything<br>
explicitly on detecting outlier loci.<br>
<br>
Many thanks,<br>
Mayte<br>
<br>
--<br>
Mayte Ruiz, Ph.D<br>
Post-doctoral Fellow<br>
University of Puerto Rico Rio Piedras<br>
<a href="mailto:mayaruizz@gmail.com">mayaruizz@gmail.com</a><br>
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Message: 2<br>
Date: Tue, 27 Nov 2012 15:48:48 +0000<br>
From: "Jombart, Thibaut" <<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>><br>
To: Mayte Ruiz <<a href="mailto:mayaruizz@gmail.com">mayaruizz@gmail.com</a>>,<br>
"<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>"<br>
<<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>><br>
Subject: Re: [adegenet-forum] detecting outliers - loci under<br>
selection<br>
Message-ID:<br>
<<a href="mailto:2CB2DA8E426F3541AB1907F98ABA657057A05092@icexch-m1.ic.ac.uk">2CB2DA8E426F3541AB1907F98ABA657057A05092@icexch-m1.ic.ac.uk</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Hi there,<br>
<br>
adegenet can be used to do a few things, R can do pretty much everything, but first we need to know what you mean by outlying loci. Do you have any trait information to relate alleles to? In any case, there will be multiple testing issue as this is possibly the worst setting for GWAS-type of analysis.<br>
<br>
Cheers<br>
<br>
Thibaut<br>
<br>
________________________________________<br>
From: <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a> [<a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>] on behalf of Mayte Ruiz [<a href="mailto:mayaruizz@gmail.com">mayaruizz@gmail.com</a>]<br>
Sent: 27 November 2012 13:58<br>
To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
Subject: [adegenet-forum] detecting outliers - loci under selection<br>
<br>
Dear Thibaut Jombart and adegenet users,<br>
<br>
I am working with RAD sequenced data of 2 populations with only 10 individuals each but with many many loci. I have been searching for a program which detects outliers (loci under selection) from my data. A colleague has suggested adegenet as a possibility. Can adegenet be used for this? I have searched the manual but do not yet find anything explicitly on detecting outlier loci.<br>
<br>
Many thanks,<br>
Mayte<br>
<br>
--<br>
Mayte Ruiz, Ph.D<br>
Post-doctoral Fellow<br>
University of Puerto Rico Rio Piedras<br>
<a href="mailto:mayaruizz@gmail.com">mayaruizz@gmail.com</a><mailto:<a href="mailto:mayaruizz@gmail.com">mayaruizz@gmail.com</a>><br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Tue, 27 Nov 2012 18:30:59 +0100<br>
From: Valeria Montano <<a href="mailto:mirainoshojo@gmail.com">mirainoshojo@gmail.com</a>><br>
To: "Jombart, Thibaut" <<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>><br>
Cc: Mayte Ruiz <<a href="mailto:mayaruizz@gmail.com">mayaruizz@gmail.com</a>>,<br>
"<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>"<br>
<<a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a>><br>
Subject: Re: [adegenet-forum] detecting outliers - loci under<br>
selection<br>
Message-ID:<br>
<CADEmh=<a href="mailto:tM2EVxwPD6sNum7EiSMESb9ZL8ZG-OpvCHcC35zTMcvw@mail.gmail.com">tM2EVxwPD6sNum7EiSMESb9ZL8ZG-OpvCHcC35zTMcvw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear Mayte,<br>
<br>
I am not sure there are many many things you can do with your many many<br>
loci. I guess you want to do a locus by locus fst and select the outliers<br>
as candidate for selective processes. I could suggest you to read this<br>
paper<<a href="http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2011.02987.x/pdf" target="_blank">http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2011.02987.x/pdf</a>><br>
to<br>
draw on from.<br>
<br>
Ciao<br>
<br>
Valeria<br>
<br>
On 27 November 2012 16:48, Jombart, Thibaut <<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>>wrote:<br>
<br>
> Hi there,<br>
><br>
> adegenet can be used to do a few things, R can do pretty much everything,<br>
> but first we need to know what you mean by outlying loci. Do you have any<br>
> trait information to relate alleles to? In any case, there will be multiple<br>
> testing issue as this is possibly the worst setting for GWAS-type of<br>
> analysis.<br>
><br>
> Cheers<br>
><br>
> Thibaut<br>
><br>
> ________________________________________<br>
> From: <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a> [<br>
> <a href="mailto:adegenet-forum-bounces@lists.r-forge.r-project.org">adegenet-forum-bounces@lists.r-forge.r-project.org</a>] on behalf of Mayte<br>
> Ruiz [<a href="mailto:mayaruizz@gmail.com">mayaruizz@gmail.com</a>]<br>
> Sent: 27 November 2012 13:58<br>
> To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>
> Subject: [adegenet-forum] detecting outliers - loci under selection<br>
><br>
> Dear Thibaut Jombart and adegenet users,<br>
><br>
> I am working with RAD sequenced data of 2 populations with only 10<br>
> individuals each but with many many loci. I have been searching for a<br>
> program which detects outliers (loci under selection) from my data. A<br>
> colleague has suggested adegenet as a possibility. Can adegenet be used<br>
> for this? I have searched the manual but do not yet find anything<br>
> explicitly on detecting outlier loci.<br>
><br>
> Many thanks,<br>
> Mayte<br>
><br>
> --<br>
> Mayte Ruiz, Ph.D<br>
> Post-doctoral Fellow<br>
> University of Puerto Rico Rio Piedras<br>
> <a href="mailto:mayaruizz@gmail.com">mayaruizz@gmail.com</a><mailto:<a href="mailto:mayaruizz@gmail.com">mayaruizz@gmail.com</a>><br>
><br>
><br>
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