[adegenet-forum] PCA with tetraploid data
avik.ray.kol at gmail.com
Mon May 9 21:00:46 CEST 2011
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.
 ON ON ON ON ON ON ON ON
> /genind2df(x, sep="/")/
Moreover, it seems extremely cumbersome for large datasets like mine
(204 indiv, 7 microsat loci); can you give any suggestion/s??
National Center for Biological Sciences
Tata Institute of Fundamental Research
Fax 91-80-2363 6662
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