[adegenet-forum] supplementary individuals

Jombart, Thibaut t.jombart at imperial.ac.uk
Fri Jun 19 12:41:27 CEST 2015

Hi Mark

I think you identified the problem. genind object keep only polymorphic sites.

You would need to 'repool' your supplementary individuals to make sure loci/alleles match, and then just extract the relevant individuals for the prediction.

Makes sense?


Dr Thibaut Jombart
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - School of Public Health
Norfolk Place, London W2 1PG, UK
Tel. : 0044 (0)20 7594 3658
Twitter: @thibautjombart

From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Mark Coulson [Mark.Coulson.ic at uhi.ac.uk]
Sent: 19 June 2015 11:23
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] supplementary individuals

Hi Thibault,

I am trying to use the pred.sup function to assign ‘test’ individuals against my baseline data. Both baseline and supplementary individuals files load fine in adegenet but when I run the pred.sup function I get the following:

Error in predict.dapc(dapc1, newdata=sup):
                Number of variables in newdata does not match original data.

Looking at the dataframes, the baseline says it’s a matrix of 1800 x 70 (which I expect), however the supplementary says 69 for the latter(?). I have found that when  interrogating @loc.fac for the supplementary file, locus27 is only listed once, while all others are listed 2x. Perhaps a coincidence but this locus is the only one that is monomorphic  in the supplementary individuals but it is polymorphic in the baseline – would this have any effect?


Inverness College UHI, a partner in the University of the Highlands and Islands www.inverness.uhi.ac.uk Board of Management of Inverness College (known as Inverness College UHI), Scottish Charity No SC021197.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20150619/f2991fc3/attachment.html>

More information about the adegenet-forum mailing list