[adegenet-forum] PCA with tetraploid data

[AVIK RAY]

Dear Dr Jombart
I want to do PCA and other analyses in adegenet, however my data is 
tetraploid dataset, 204 individuals, 7 microsatellite loci, so it is not 
read using read.structure (as you mentioned in your earlier mails to 
Sarah Castillo (19/10/2010, RE: Looking for help with a PCA using 
adegenet in R);

So far I've understood from the code is instead of coding each 
individual for each locus as in read.structure (diploid data) idea is to 
get the allele freq for each allele (whether present or absent) and then 
code each individual genotypes accordingly, However, I did not get the 
last part of the code, e.g.

.............

$pop

[1] ON ON ON ON ON ON ON ON

Levels: ON

 > /genind2df(x, sep="/")/

pop gen

...............

Moreover, it seems extremely cumbersome for large datasets like mine 
(204 indiv, 7 microsat loci); can you give any suggestion/s??

Thanks

best regards

AVIK

  --

AVIK RAY
Visiting Fellow
National Center for Biological Sciences
Tata Institute of Fundamental Research
GKVK Campus
Bellary Road
Bangalore-560065
India
Ph 91-80-23666340
Fax 91-80-2363 6662

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