[adegenet-forum] clones in sPCA adegenet

[Martin]

Hello all,


I’m new to adegenet and was wondering if I could ask for
some advice.  I’m working with a dataset
of microsatellite markers from a haploid fungus which reproduces both asexually
and sexually (it seems).  Therefore the
dataset has many clones which can be present in many locations.  I am looking to do a sPCA and was wondering
if the clonality in the dataset will influence the sPCA.  I cannot use the clone-corrected dataset
because a single clone can be present in many locations.  Does anyone have any experience of this? Will
a sPCA with many clones still produce reliable results?  I can’t think why not but maybe I’m missing
something.


Also, a more technical question. I see a cline with a
distinct group (particularly clear when using colorplot).  Is there any way to draw out the groups from
the sPCA?  I assume it is in the $ls or
$li component of the sPCA output but looking at these the cutoff is nowhere as
clear as on the graphical output.


Thank you in advance, and sorry if the questions are too
simplistic.


Martin

 		 	   		  
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