[adegenet-forum] detecting outliers - loci under selection (Valeria Montano)
Valeria Montano
mirainoshojo at gmail.com
Tue Dec 4 10:45:47 CET 2012
Thanks Fre for this nice email object :-) it reads like I am a locus under
selection!
On 4 December 2012 09:00, Frederik Van den Broeck <
Frederik.VandenBroeck at bio.kuleuven.be> wrote:
> Lositan or Bayescan are easy to use and will do the job!
>
> Fre
>
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> Today's Topics:
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> 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)
>
>
> ----------------------------------------------------------------------
>
> 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
> Message-ID:
> <CABBTkLa6w1JOt_ci7aWmyuF1_C=iV6VOXRaN2P_+q=
> whAfZCAQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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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