[adegenet-forum] Allele frequencies around 0.5

[Niklas Tysklind]

Dear Thibaut,

Many thanks for your help before. I've solved my previous "mistery 
structuring". I exported the sample$li values and susequetly divided my 
data acording to these "rogue" groups, and reanalysed. As it happens, it 
was due to one microsat locus with very low diversity (6 alleles with 2 
very dominant ones), thus the data was being sorted according to whether 
individuals were homozygous to one or another allele or heterozygosous 
for both. Very neat!! and I'm very happy it nothing more serious to 
worry about! when I remove that locus, then the PCA looks more like a 
cloud of dots (as I was expecting).

However, as you point out in Jombart et al, 2009, problems may arise 
when frequencies are near 0.5 and thus I would like to recalculate my 
PCAs and CAs.  You suggest dividing allele frequencies (fj)  by 
(fj(1-fj))^0.5, however, genind and genpop objects store locus 
information by allele counts rather than frequencies. Do you have any 
suggestions about how to go about to do such a transformation in adegenet?

Kind regards,

Niklas

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