[adegenet-forum] Loci selection for SNP data

[Thibaut Jombart]

Hi there,

no, the position of the loci is not needed. This retains most contributing
alleles, no matter what the loci are.

Best
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
Head of RECON: repidemicsconsortium.org
WHO Consultant - outbreak analysis
sites.google.com/site/thibautjombart/
Twitter: @TeebzR
+44(0)20 7594 3658

On 12 September 2017 at 22:19, Ngoc-Tien Tran <Ngoc-Tien.Tran at insa-rennes.fr
> wrote:

> Hello ,
> Thank you so much for your suggestion.
> However, this method only works if the position on the chromosomes are
> available for each locus. Am I correct ?
>
> Best wishes !
> Ngoc-Tien
>
> ----- Mail original -----
> De: "thibautjombart" <thibautjombart at gmail.com>
> À: "Ngoc-Tien Tran" <Ngoc-Tien.Tran at insa-rennes.fr>
> Cc: "adegenet-forum" <adegenet-forum at lists.r-forge.r-project.org>
> Envoyé: Lundi 11 Septembre 2017 14:05:46
> Objet: Re: [adegenet-forum] Loci selection for SNP data
>
> Hello,
>
> there is no tool specifically dedicated to this, but you could run a PCA,
> retain axes corresponding to the xxx% of variance, and then keep only the
> alleles contributing most to these axes. Here's a quick example:
>
> > data(sim2pop)
> > pca1 <- dudi.pca(tab(sim2pop), scannf = FALSE, nf = 3)
> > contrib <- pca1$c1^2
> > which(contrib > 0.01, TRUE)  # contrib > 1%
>        row col
> L02.06  21   1
> L04.02  47   1
> L05.02  60   1
> L05.09  67   1
> L06.6   74   1
> L07.7   84   1
> L08.07  91   1
> L09.8  102   1
> L09.9  103   1
> L10.01 104   1
> L10.12 115   1
>
> [...]
>
> Best
> Thibaut
>
>
> --
> Dr Thibaut Jombart
> Lecturer, Department of Infectious Disease Epidemiology, Imperial College
> London
> Head of RECON: repidemicsconsortium.org
> WHO Consultant - outbreak analysis
> sites.google.com/site/thibautjombart/
> Twitter: @TeebzR
> +44(0)20 7594 3658
>
> On 7 August 2017 at 13:45, Ngoc-Tien Tran <Ngoc-Tien.Tran at insa-rennes.fr>
> wrote:
>
> > Hello,
> > I'm working with SNP data with a large number of loci.
> > I would like to know if there is a tool in the package "adegenet"
> allowing
> > me to select just one smaller set of loci without loosing information.
> >
> > Thanks for your help !
> > Best wishes,
> > Ngoc-Tien
> >
> >
> > --
> > --------------------------------------------------------------
> > TRAN Ngoc-Tien
> > Département Génie Mathématiques/Analyse de Risque et Optimisation et
> > Modélisation.
> > INSA-Rennes
> > Tel : +33.(0)7.51.57.96.53
> > @mail : ngoc-tien.tran at insa-rennes.fr
> > _______________________________________________
> > adegenet-forum mailing list
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> > listinfo/adegenet-forum
> --
> --------------------------------------------------------------
> TRAN Ngoc-Tien
> Département Génie Mathématiques/Analyse de Risque et Optimisation et
> Modélisation.
> INSA-Rennes
> Tel : +33.(0)7.51.57.96.53
> @mail : ngoc-tien.tran at insa-rennes.fr
>
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