[adegenet-forum] SNP data and PCA

[Tagliamonte,Massimiliano S]

Dear Adegenet users,


I am trying to perform a PCA on whole genome SNP data, and the results I have so far seem to make sense. I do have a few doubts though, and I may need some help to solve them.


Following variant calling, I converted my data to a dataframe, e.g:

mysnps<- data.frame('ind_names'= c('s1', 's2', 's3'), 'locus1'=c('A/A', 'N', 'A/G'), 'locus2'=c('G/G', 'A/G', A/A'))

Then I used df2genind on the dataframe, and performed the principal component analysis.

Was that right? I am still not sure if I should have rather used a genlight object. Should I change it if I decide to do DAPC or PCoA?


Thanks for your kind help,

Max


Massimiliano S. Tagliamonte
Graduate Student
University of Florida
College of Veterinary Medicine
Department of Infectious Diseases and Pathology
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