[adegenet-forum] Cluster specific alleles

[Jombart, Thibaut]

Dear Michèle, 

sorry about the late reply - just coming back from a workshop. 
You can find the most contributing alleles using the loadingplot (see vignette on DAPC, p.17 and further). However, this will only tell you which alleles allow to discriminate the groups, without telling you which allele precisely belongs to which group. Further analysis is needed, but here is an example. 

### R code ###
## generate DAPC example
library(adegenet)
example(dapc)
scatter(dapc1) # this example uses 'microbov' - cattle microsat dataset

## visualize variable contributions
loadingplot(dapc1$var.contr)
x <- loadingplot(dapc1$var.contr, thres=.02) # thresold defined based on previous plot

## list most contributing variables
x

## get table of allele frequencies for the selected alleles
tab <- apply(truenames(microbov)$tab[, x$var.names],2, function(e) tapply(e, pop(microbov), mean,na.rm=TRUE)) # replace 'microbov' by your dataset

## visualize this table
table.value(tab, col.lab=colnames(tab))

### end R code ###

Here you can see that some of the alleles discriminate two large taxonomic groups (Bos taurus vs Bos indicus) but some are also more specific, e.g. CSRM60.093

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 michele.lerch at wsl.ch [michele.lerch at wsl.ch]
Sent: 31 January 2014 10:00
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] Cluster specific alleles

Hello,

I have a question concerning DAPC. I would like to know which alleles are characheristic to which cluster. How can I get this information?
Thanks for your answer,
Michèle