[adegenet-forum] allelic dosage for a polyploid

[Bernadette Julier]

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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