[adegenet-forum] adegenet-forum Digest, Vol 70, Issue 7

[Manuela]

Patrícia,



I made a small test with example suggested on sPCA tutorial (
http://adegenet.r-forge.r-project.org/) and apparently it seems that you
can get the SNP loadings after modelling yout dataset by DAPC. The values
you want are stored in the slot pca.loadings.


Just try these two command lines:

A<-dapc1$pca.loadings

write.table(A,file=”A”)


And afterwards open it in Excel. By default a file named “A” is saved on
MyDocuments folder. But if you have any trouble on open it please let me
now directly to my e-mail. Anyway, I’m sure Dr. Thimbault will soon confirm
this information.


Hoping to be helpful,

M.


2014-06-14 11:00 GMT+01:00 <
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>    1. DAPC: loadings of original variables as table? (Patricia Salerno)
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>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 13 Jun 2014 16:27:10 -0500
> From: Patricia Salerno <patriciasalerno at gmail.com>
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: [adegenet-forum] DAPC: loadings of original variables as
>         table?
> Message-ID:
>         <CAHKShSk7zN-6-o35eTHGJ=fE_JVGQMQSxhbKDh=
> 531Ejp3VQEw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> 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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