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

[Patricia Salerno]

Thank you so much, Manuela, for the tip and for the reference!! very
helpful... worked just fine with my data.


Cheers!!

~patricia.






On Sat, Jun 14, 2014 at 11:09 AM, Manuela <manuelacorreia2 at gmail.com> wrote:

>
>
> Patrícia,
>
> About this same subject I would like to recommend you an article I've read
> some time ago.
>
> Reference:
> Kalinowski, ST (2011) "The computer program STRUCTURE does not reliably
> identify the main genetic clusters within species: simulations and
> implications for human population structure", Heredity, 106 :625-632
>
> Cheers,
> M.
>
>
> 2014-06-14 17:00 GMT+01:00 Manuela <manuelacorreia2 at gmail.com>:
>
> 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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>>
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-- 
Patricia Salerno
PhD Candidate
Ecology Evolution and Behavior
Section of Integrative Biology
University of Texas at Austin
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