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

[Manuela]

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:
>>>
>>>    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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