[adegenet-forum] DAPC and morphological data

[Jombart, Thibaut]

Hello, 

your data are not genetic markers, and your input is not compatible at all with what df2genind expects.

DAPC is implemented for data.frames and matrices. Here, you should use something along the lines of 

dapca1 <- dapc(jeu[,-1], grp=jeu[,1])

Cheers
Thibaut
______________jeu__________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Maéva Angélique TECHER [maeva-angelique.techer at cirad.fr]
Sent: 27 May 2015 08:41
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] DAPC and morphological data

Dear all,

I'm trying to perform a DAPC on a morphological dataset which is composed of 176 variables of distances for several populations.

The dataset looks like this:

> head(jeu)
      POP   X1.2   X1.3   X1.4   X1.5   X1.6   X1.7   X1.8   X1.9  X1.10  X1.11  X1.12  X1.13  X1.14  X1.15  X1.16  X1.17  X1.18  X1.19   X2.3   X2.4   X2.5   X2.6   X2.7   X2.8   X2.9  X2.10
CAF1.1 CAF 0.0837 0.2564 0.3150 0.3667 0.3266 0.2661 0.1942 0.1823 0.1133 0.1667 0.1409 0.2364 0.3959 0.7171 0.5261 0.4894 0.3896 0.4618 0.1742 0.2350 0.2841 0.2773 0.2304 0.1756 0.2089 0.1411

I tried to input the matrix in R using Adegenet and the function df2genind. My problem is that R stopped the importation and posted this message:

> morpho<-df2genind(jeu[,1:177], missing = 0, ploidy = 1, type = "codom")
Error: C stack usage is too close to the limit


Is the problem coming from the variables which are not integers or from the importation script?

Thank you very much for your help,
Cheers,
Maéva


--


Maéva TECHER
Doctorante en Génétique des Populations / Ph.D Student in Population Genetics
"Diversité génétique et phylogéographie de l'abeille Apis mellifera dans la zone Océan Indien"
UMR PVBMT, Université de La Réunion - CIRAD

7 chemin de l'IRAT Ligne Paradis,
97410 Saint Pierre,
La Réunion ,
Tel: +262 262 49 92 41
Portable: +262 692 05 13 07
maeva-angelique.techer at cirad.fr
maeva.techer at hotmail.fr







_______________________________________________
adegenet-forum mailing list
adegenet-forum at lists.r-forge.r-project.org
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum