[adegenet-forum] DAPC: Allele counts vs Allele frequencies

[Thibaut Jombart]

For genind objects, this is done automatically (under the hood, scaleGen
scales allele frequencies). If you use 'tab()' to extract allelic profiles,
just use tab(freq = TRUE) to get frequencies.

Best
Thibaut

--
Dr Thibaut Jombart
Software Design and Implementation Lead, Data.Org
Senior Lecturer in Outbreak Analytics, Imperial College London
President of RECON: repidemicsconsortium.org
https://thibautjombart.netlify.com
Twitter: @TeebzR



On Wed, 3 Aug 2022 at 17:16, André Boler Barros <andrebolerbarros at gmail.com>
wrote:

> Thanks Thibaut!
>
> Another question: Is it required to adapt the pipeline present in the
> tutorial for DAPC to having the data in frequencies?
>
> *André Boler Barros*
>
>
> Em qua., 3 de ago. de 2022 às 16:07, Thibaut Jombart <
> thibautjombart at gmail.com> escreveu:
>
>> Dear André
>>
>> it should not make any difference as long as all loci have the same
>> ploidy. If not, then I would recommend using frequencies to avoid
>> over-weighting loci with higher ploidy.
>>
>> Best
>> Thibaut
>>
>> --
>> Dr Thibaut Jombart
>> Software Design and Implementation Lead, Data.Org
>> Senior Lecturer in Outbreak Analytics, Imperial College London
>> President of RECON: repidemicsconsortium.org
>> https://thibautjombart.netlify.com
>> Twitter: @TeebzR
>>
>>
>>
>> On Wed, 3 Aug 2022 at 10:25, André Boler Barros <
>> andrebolerbarros at gmail.com> wrote:
>>
>>> Hi everyone,
>>>
>>> I would like to know if I should transform my allele counts in
>>> frequencies prior to using DAPC or if I should use the allele counts.
>>>
>>> Thanks,
>>>
>>> *André Boler Barros*
>>> _______________________________________________
>>> adegenet-forum mailing list
>>> adegenet-forum at lists.r-forge.r-project.org
>>>
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum
>>
>>
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