[adegenet-forum] supplementary individuals

[Jombart, Thibaut]

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?

Best
Thibaut


==============================
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
http://sites.google.com/site/thibautjombart/
http://sites.google.com/site/therepiproject/
http://adegenet.r-forge.r-project.org/
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?

Suggestions?

Thanks,
Mark
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.
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