[adegenet-forum] removing groups of individuals from genind object

Jombart, Thibaut t.jombart at imperial.ac.uk
Wed Dec 3 14:57:25 CET 2014

Hi there,

genind objects can be subsetted like matrices, e.g. x[foo, ]
where foo is a subset of individuals. Should be documented in the adegenet basics tutorial.


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 [coulsonmw at gmail.com]
Sent: 03 December 2014 13:53
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] removing groups of individuals from genind object


This is probably quite simple, but I have done a DAPC on a large number of samples (~300) and have found quite good separation between samples from a couple of very unique sites and the rest of the dataset. I'd like to now run another DAPC on just the remaining samples (i.e. kick out the most distinct groups) and am wondering how to easiest remove whole samples of individuals from the genind file (say pop70-pop100), rather than having to make a separate input file. I think I could do this with a normal dataframe but not sure about a genind object??

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