[adegenet-forum] redefining populations and excluding populations

[Zhian Kamvar]

For the populations, you can also use the pop argument in the brackets.
The previous example would look like this:

y <- microbov[pop = !popNames(microbov) %in% "Salers"]

You can also use strings or integers.

- Zhian


> Date: Fri, 5 Aug 2016 12:47:38 +0100
> From: Thibaut Jombart <thibautjombart at gmail.com>
> To: Mark Coulson <Mark.Coulson.ic at uhi.ac.uk>
> Cc: "adegenet-forum at lists.r-forge.r-project.org"
> 	<adegenet-forum at lists.r-forge.r-project.org>
> Subject: Re: [adegenet-forum] redefining populations and excluding
> 	populations
> Message-ID:
> 	<CANPRA+oLiq534F-+7-Qs_QE3kZc5_oB+7WfYuGuqs8_fywoy6w at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi there,
> 
> most handling is documented:
> adegenetTutorial("basics")
> 
> section 5.1. See also the manpage for most accessors:
> ?nLoc
> 
> For instance, to exclude the Salers from microbov:
> x <- microbov[i=!as.character(pop(microbov)) %in% c("Salers")]
> 
> Cheers
> Thibaut
> 
> 
> --
> Dr Thibaut Jombart
> Lecturer, Department of Infectious Disease Epidemiology
> Imperial College London
> https://sites.google.com/site/thibautjombart/
> https://github.com/thibautjombart
> Twitter: @TeebzR <https://twitter.com/TeebzR>
> 
> On 5 August 2016 at 09:15, Mark Coulson <Mark.Coulson.ic at uhi.ac.uk> wrote:
> 
>> I have a genind file with an @pop factor however based on various cluster
>> analysis I have redefined 4 groups (instead of the initial 12). I want to
>> assign this grouping factor to my genind object and then eliminate one of
>> the groups for subsequent analysis (presumably using the poppr package).
>> How do I go about this?
>> 
>> 
>> 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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