[adegenet-forum] detecting outliers - loci under selection (Valeria Montano)
Frederik Van den Broeck
Frederik.VandenBroeck at bio.kuleuven.be
Tue Dec 4 10:00:35 CET 2012
Lositan or Bayescan are easy to use and will do the job!
Fre
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Today's Topics:
1. detecting outliers - loci under selection (Mayte Ruiz)
2. Re: detecting outliers - loci under selection (Jombart, Thibaut)
3. Re: detecting outliers - loci under selection (Valeria Montano)
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Message: 1
Date: Tue, 27 Nov 2012 09:58:21 -0400
From: Mayte Ruiz <mayaruizz at gmail.com>
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] detecting outliers - loci under selection
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<CABBTkLa6w1JOt_ci7aWmyuF1_C=iV6VOXRaN2P_+q=whAfZCAQ at mail.gmail.com>
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Dear Thibaut Jombart and adegenet users,
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.
Many thanks,
Mayte
--
Mayte Ruiz, Ph.D
Post-doctoral Fellow
University of Puerto Rico Rio Piedras
mayaruizz at gmail.com
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Message: 2
Date: Tue, 27 Nov 2012 15:48:48 +0000
From: "Jombart, Thibaut" <t.jombart at imperial.ac.uk>
To: Mayte Ruiz <mayaruizz at gmail.com>,
"adegenet-forum at lists.r-forge.r-project.org"
<adegenet-forum at lists.r-forge.r-project.org>
Subject: Re: [adegenet-forum] detecting outliers - loci under
selection
Message-ID:
<2CB2DA8E426F3541AB1907F98ABA657057A05092 at icexch-m1.ic.ac.uk>
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Hi there,
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.
Cheers
Thibaut
________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Mayte Ruiz [mayaruizz at gmail.com]
Sent: 27 November 2012 13:58
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] detecting outliers - loci under selection
Dear Thibaut Jombart and adegenet users,
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.
Many thanks,
Mayte
--
Mayte Ruiz, Ph.D
Post-doctoral Fellow
University of Puerto Rico Rio Piedras
mayaruizz at gmail.com<mailto:mayaruizz at gmail.com>
------------------------------
Message: 3
Date: Tue, 27 Nov 2012 18:30:59 +0100
From: Valeria Montano <mirainoshojo at gmail.com>
To: "Jombart, Thibaut" <t.jombart at imperial.ac.uk>
Cc: Mayte Ruiz <mayaruizz at gmail.com>,
"adegenet-forum at lists.r-forge.r-project.org"
<adegenet-forum at lists.r-forge.r-project.org>
Subject: Re: [adegenet-forum] detecting outliers - loci under
selection
Message-ID:
<CADEmh=tM2EVxwPD6sNum7EiSMESb9ZL8ZG-OpvCHcC35zTMcvw at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear Mayte,
I am not sure there are many many things you can do with your many many
loci. I guess you want to do a locus by locus fst and select the outliers
as candidate for selective processes. I could suggest you to read this
paper<http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2011.02987.x/pdf>
to
draw on from.
Ciao
Valeria
On 27 November 2012 16:48, Jombart, Thibaut <t.jombart at imperial.ac.uk>wrote:
> Hi there,
>
> 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.
>
> Cheers
>
> Thibaut
>
> ________________________________________
> From: adegenet-forum-bounces at lists.r-forge.r-project.org [
> adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Mayte
> Ruiz [mayaruizz at gmail.com]
> Sent: 27 November 2012 13:58
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: [adegenet-forum] detecting outliers - loci under selection
>
> Dear Thibaut Jombart and adegenet users,
>
> 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.
>
> Many thanks,
> Mayte
>
> --
> Mayte Ruiz, Ph.D
> Post-doctoral Fellow
> University of Puerto Rico Rio Piedras
> mayaruizz at gmail.com<mailto:mayaruizz at gmail.com>
>
>
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum
>
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