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<DIV><FONT face=Arial>Yu-Huang Wang wrote:<BR>> Dear Dr.
Jombart,<BR>> <BR>> I used AFLP to study the landscape genetics
of <SPAN class=446350514-25062008>spiny</SPAN> rat. I tried to
<BR>> identify the position of its genetic boundaries and overlay the
<BR>> boundaries with potential dispersal barriers (highway, river,
etc.).<BR>> I have tried 'wombsoft' but there is still some subjectivity of
<BR>> defining genetic bandwidth. I read through the manual of
adegenet.<BR>> It seems that AFLP data can not be used for the sPCA in
adegenet. <BR>> Will you include the function of using AFLP data for
adegenet in the <BR>> near future?<BR>> <BR>> Best
regards,<BR>> <BR>> Yu-Huang Wang<BR>> PhD. Candidate<BR>>
Dep. Life Science<BR>> Tung-Hai University<BR>> Taichung City<BR>>
Taiwan<BR>> <BR>> <BR>Dear Yu-Huang,</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial>Thanks for your interest in adegenet and the sPCA. their
are no theoretical reason why the sPCA could not be used with AFLP, but you may
be right about the current implementation: AFLP may not be read as easliy as
other data. One way is to read your data inside R as a genotypes X alleles
matrix, containing 1 where the genotype possesses the given allele, and 0
elsewhere. Then you can use this as input to the 'genind' constructor (see
?genind) to get a genind object. And then, provided your xy coordinates are
sorted the same way as your genotypes, the sPCA can be used without
problem.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial>Your question is interesting, and may be (will surely be)
asked by other users. It would be nice if you could post your next questions on
the adegenet-forum, which is dedicated to these topics:<BR><A
href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</A></FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial>As soon as I have time, I will add a section in the
tutorial about reading AFLP in adegenet. If you have any problem, please do not
hesitate to post on the ML.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial>Best regards,</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial>Thibaut.<BR></FONT></DIV></BODY></HTML>