[adegenet-forum] DAPC

Jombart, Thibaut t.jombart at imperial.ac.uk
Wed Mar 28 12:36:22 CEST 2012


what is the size of the genind object - how many individuals and alleles?
The threshold for polymorphism seems a bit high. Does setting it to zero help?
Otherwise, try lowering down max.n.clust.
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of josé manuel lucas cánovas [josemanuel.lc at hotmail.com]
Sent: 28 March 2012 11:19
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] DAPC


I'm trying to do a DAPC with a sequence matrix of mtDNA. I have 89 sequences (they collapsed in 7 haplotypes) and this is my batch:

setwd ("C:\\Users\\......")
library (MASS)
read.dna ("xxx.fasta", format="fasta")->x
DNAbin2genind(x, polyThres = 0.01)->xSNP
find.clusters(xSNP, choose.n.clust=FALSE,criterion="diffNgroup", clust=NULL)->cls_x

In this point, I should choose the number PC's to retain (>=1) but any chosen number I always obtain the following response:

Error en kmeans(XU, centers = nbClust[i], iter.max = n.iter, nstart = n.start) :
  more cluster centers than distinct data points.

I know my data set show little variation, I don't know if it could produce such a result...

Please, someone can help me?

Thanks in advance!!

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