[adegenet-forum] DAPC and Allele Contribution

Bernhard Stoeckle berniestoeckle at gmx.de
Thu Mar 8 12:17:05 CET 2012

Hallo Dr. Jombart and Adegenet users,


I have a question regarding DAPC. The subject I am interested in was not absolutely clear to me when I was reading the manual and the tutorials. Maybe I missed something. If so, I am sorry.


I have a dataset of 1800 individuals genotyped with 12 microsatellites. In order to visualize the genetic Population structure I made a Discriminant Analysis of Principal Components (DAPC) without "find.clusters" and it worked perfect. Because I am interested in the alleles which have the most contribution to the DAPC I visualized the contributions of alleles with the command: "#loadingplot(dapc1$var.contr)".


I received a data frame with the contributions of the alleles. My question: Does this data frame show the contributions of the alleles to the complete DAPC (PCA and DA) or just to the PCA? 


Thank you so much in advance,


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