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

[Manuela]

Sorry, I meant DAPC tutorial (March 24,2014).

Cheers,
M.


2014-06-14 16:56 GMT+01:00 Manuela <manuelacorreia2 at gmail.com>:

> 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 <
> adegenet-forum-request at lists.r-forge.r-project.org>:
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>> Today's Topics:
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>>    1. DAPC: loadings of original variables as table? (Patricia Salerno)
>>
>>
>> ----------------------------------------------------------------------
>>
>> 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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