[adegenet-forum] Loci selection for SNP data

[Ngoc-Tien Tran]

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
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-- 
-------------------------------------------------------------- 
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