[adegenet-forum] DAPC and Allele Contribution

Jombart, Thibaut t.jombart at imperial.ac.uk
Thu Mar 8 12:34:52 CET 2012


$var.contr gives the contribution of the alleles (in row) to each discriminant function, i.e. principal components of the DAPC (columns).

If you run example(dapc) and then:
> head(dapc1$var.contr)
                    LD1          LD2          LD3          LD4          LD5
INRA63.167 9.749327e-07 3.000172e-06 4.471260e-07 4.358236e-08 1.342053e-05
INRA63.171 9.470378e-07 2.648038e-06 6.247767e-06 1.588937e-07 9.007806e-07
INRA63.173 4.493032e-05 1.585300e-05 8.049491e-05 4.627630e-06 1.289250e-04
INRA63.175 2.773575e-02 2.067440e-03 4.908576e-03 1.824390e-02 9.547637e-03
INRA63.177 1.587367e-03 1.250083e-02 1.453551e-02 2.458131e-02 3.460852e-03
INRA63.179 5.863705e-04 2.016185e-05 1.397237e-04 5.121410e-03 5.504677e-03

The first column given allele contributions to the first axis, the second to the second axis, etc.



From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of Bernhard Stoeckle [berniestoeckle at gmx.de]
Sent: 08 March 2012 11:17
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] DAPC and Allele Contribution

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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