[adegenet-forum] Spatial DAPC

Jombart, Thibaut t.jombart at imperial.ac.uk
Tue Aug 28 11:50:19 CEST 2012


using spatial information to define clusters is a usual practice, but then for further genetic analysis, it is best if the criteria defining the clusters is purely spatial. I would run a clustering algorithm based on the spatial coordinates, define groups, and then input them in DAPC. 

DAPC uses PCA prior to DA to reduce the dimension of the input space and decorrelate the variables; sPCA should not be used as a replacement as its PCs are usually not uncorrelated.


From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Matt Warren [matt.james.warren at gmail.com]
Sent: 24 August 2012 18:10
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] Spatial DAPC


Is there a way to incorporate geographic coordinates in a DAPC, such as transforming allele frequencies with sPCA rather than PCA, and then running find.clusters?


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