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Dear Dr Jombart<br>
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);
<p class="MsoNormal">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.</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height:
normal;">………….</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height:
normal;">$pop</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height:
normal;">[1] ON ON ON ON ON ON ON
ON</p>
<p class="MsoNormal">Levels: ON</p>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height:
normal;">> <i>genind2df(x,
sep="/")</i></p>
<p class="MsoNormal">pop gen</p>
<p class="MsoNormal">……………</p>
<p class="MsoNormal">Moreover, it seems extremely cumbersome for
large datasets
like mine (204 indiv, 7 microsat loci); can you give any
suggestion/s??</p>
<p class="MsoNormal">Thanks</p>
<p class="MsoNormal">best regards</p>
<p class="MsoNormal">AVIK <br>
</p>
<p class="MsoNormal"> -- <br>
</p>
<pre class="moz-signature" cols="72">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
</pre>
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