[adegenet-forum] allelic dosage for a polyploid

[Thibaut Jombart]

Hi there,

If I understand well, your data are binary, so you could go directly for a
matrix of binary data. Let 'dat' be your matrix of codes (0-4):

x <- 1 * dat>0
dapc1 <- dapc(x, ...) # make sure you pass a group here.

The genind class would only add an extra complexity here.

Best
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
Head of RECON: repidemicsconsortium.org
sites.google.com/site/thibautjombart/
github.com/thibautjombart
Twitter: @TeebzR <http://twitter.com/TeebzR>

On 25 October 2016 at 14:10, Bernadette Julier <bernadette.julier at inra.fr>
wrote:

> Hello,
>
>
>
> I have SNP data on an autotetraploid species. They have been coded as
> dominant markers but with the dose. It means that for each SNP in each
> individual, I have:
>
> 0: absence
>
> 1: presence in 1 dose
>
> 2: presence in 1 dose
>
> 3: presence in 1 dose
>
> 4: presence in 1 dose
>
>
>
> Is it correct if I write:
>
> df2genind(file[,-c(1)], ploidy=4, sep="", type="PA", pop=X$pop)
>
>
>
> Can dapc procedure be used on this dataset ? I could transform the dataset
> into 0 and 1 (presence in any dose) but it would be a loss of information.
>
>
>
> Thanks for any advice
>
>
>
> Bernadette
>
> INRA Lusignan, France
>
>
>
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