[adegenet-forum] DAPC: loadings of original variables as table?

[Patricia Salerno]

Hi everyone,

I'm using PCA/DAPC as well as STRUCTURE with a SNP matrix. I'm getting
different results with the two approaches, and the DAPC results are much
more logical, biologically speaking (some individuals of a very
well-supported cluster in DAPC are being assigned to the other cluster,
even though the separation in PC1 is enormous!). Thus, I want to see if the
discrepancies of population assignment in STRUCTURE are due to the fact
that the DAPC initially transforms the data into vectors that maximize
variation, thus effectively weighing my variables differently, while
STRUCTURE weighs all SNPs equally. The only strategy I've come up with to
investigate this issue further is to generate a table of the loadings of
the SNP variables (the original, not the transformed variables after PCA),
and prune my matrix to only keep the SNPs with sufficient contributions
(setting some post-hoc cutoff). However, I cannot figure out how to print a
table of the SNP loadings after the DAPC, or if it's even possible. What I
would want is a printed matrix of two columns, one with the SNP names, and
another with the contributions/loadings. Could anyone help me with this?
Or, does anyone have another suggestion for approaching this issue?

Thank you!!

~patricia.


-- 
Patricia Salerno
PhD Candidate
Ecology Evolution and Behavior
Section of Integrative Biology
University of Texas at Austin
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