[adegenet-forum] Reading SNP data as a genind oblect

[Jombart, Thibaut]

Yes, for now, sPCA is not implemented for genlight objects.

What is the size of your dataset?

Cheers

Thibaut
________________________________________
From: Grant Gillis [grant.j.gillis at gmail.com]
Sent: 21 June 2012 16:31
To: Jombart, Thibaut
Cc: adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] Reading SNP data as a genind oblect

Great.  Thanks!

As a follow up.  I had hoped to do an spca on my SNP data but it seems to be just too big for the memory.  I haven't been able to find out whether it is possible to do an spca on a genlight oblect.  It appears not to be.  Is this true?

Many thanks again.

On 21 June 2012 14:26, Jombart, Thibaut <t.jombart at imperial.ac.uk<mailto:t.jombart at imperial.ac.uk>> wrote:
Hello,

the problems comes from the format of the raw data. Two alleles from a given locus should be a single column, possibly with a separator such as "/". Here, alleles are on separate columns.

Cheers

Thibaut

--
######################################
Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - School of Public Health
St Mary’s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jombart at imperial.ac.uk<mailto:t.jombart at imperial.ac.uk>
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/
________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:adegenet-forum-bounces at lists.r-forge.r-project.org> [adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:adegenet-forum-bounces at lists.r-forge.r-project.org>] on behalf of Grant Gillis [grant.j.gillis at gmail.com<mailto:grant.j.gillis at gmail.com>]
Sent: 21 June 2012 13:22
To: adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>
Subject: [adegenet-forum] Reading SNP data as a genind oblect

Dear List,

I have SNP data structured as below.  This seems to be accepted as a genind object however the obj at tab suggests to me something strange is going on.  Too many alleles per locus.  Any tips as to where I'm going wrong would be much appreciated.

Cheers,
Grant



> dat <- structure(c("A", "A", "A", "G", "G", "G", "A", "G", "NA", "G",
+ "G", "NA", "A", "A", "A", "A", "G", "A", "A", "C", "A", "A",
+ "C", "C"), .Dim = c(3L, 8L), .Dimnames = list(c("genot. 1", "genot. 2",
+ "genot. 3"), c("1", "1", "2", "2", "3", "3", "4", "4")))


        1   1   2    2    3   3   4   4
genot. 1 "A" "G" "A"  "G"  "A" "A" "A" "A"
genot. 2 "A" "G" "G"  "G"  "A" "G" "C" "C"
genot. 3 "A" "G" "NA" "NA" "A" "A" "A" "C"
>
>
>


> obj <- df2genind(dat, ploidy=2, missing = NA)
>
>
> obj at tab
 L1.1 L1.2 L1.3 L1.4 L2.1 L2.2 L2.3 L2.4 L2.5 L3.1 L3.2 L3.3 L3.4 L3.5 L4.1 L4.2 L4.3 L4.4 L4.5 L4.6
1  0.5  0.5  0.5  0.5  0.5  0.5  0.0  0.5  0.5  0.5  0.5  0.5  0.5  0.0  0.5  0.5  0.0  0.5  0.5  0.0
2  0.5  0.5  0.5  0.5  0.5  0.0  0.5  0.5  0.5  0.5  0.5  0.5  0.0  0.5  0.5  0.0  0.5  0.5  0.0  0.5
3  0.5  0.5  0.5  0.5   NA   NA   NA   NA   NA  0.5  0.5  0.5  0.5  0.0  0.5  0.5  0.0  0.5  0.0  0.5