[adegenet-forum] dapc on allele frequencies

[Thibaut Jombart]

Hi Mark,

in principle you could use genlight, setting the ploidy for each pool to
(the number of individuals) * ploidy. It should still be quite efficient in
terms of memory savings, and run decently fast for a small number of pools
(<100).

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 17 May 2017 at 16:48, Mark Coulson <coulsonmw at gmail.com> wrote:

> Hi
>
>
>
> I have allele frequency data for pools of individuals (no individual
> genotype data) for >500,000 SNPs. I know I can do a dapc on allele
> frequencies directly but given this many SNPs should I be using a
> ‘genlight’ object or is this only for individual genotypes?
>
>
>
> Thanks,
>
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