[adegenet-forum] Analyzing a genetic distance matrix in DAPC

[Jombart, Thibaut]

Dear Erik, 

you can't, not directly anyway, but as a trick you can feed dapc the principal components (all of them) of a principal coordinate analysis / MDS. See the function dudi.pco in ade4. Assuming pco1 is the output of dudi.pco on your distance matrix, you want to use the coordinates in pco1$li as input to DAPC. 

All the best
Thibaut

--
######################################
Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - School of Public Health
St Mary’s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jombart at imperial.ac.uk
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/
________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Sotka, Erik [SotkaE at cofc.edu]
Sent: 15 July 2013 04:04
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] Analyzing a genetic distance matrix in DAPC

Hello!  I would like to know if it were possible to enter a genetic distance matrix into the DAPC analysis.  The matrix contains Bruvo distances, useful for a species with mixed ploidy in the same population.  All of the tutorials and examples I can find enter raw genetic data into find.clusters() or dapc().
Thank you!
Erik




--
Erik Sotka
Associate Professor of Biology, College of Charleston
Grice Marine Laboratory, 205 Fort Johnson Road, Charleston, SC  29412
Office: 843-953-9191
eMail: SotkaE at cofc.edu
www.MarineEvolutionaryEcology.org

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