[adegenet-forum] pop argument

[Tom Devitt]

Thanks for your reply, Thibaut.

But how do I do this if I have a separate text file of population names corresponding to the individuals listed in the FASTA file? I can load the file of population names using read.table, but then I'm not sure how to use the pop argument from there.

When I tried:

> x <-("~/path/file.txt")
> pop(x)

I get: 

Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "pop", for signature "character"

Sorry, just learning R . . .


On Aug 24, 2012, at 8:54 AM, Jombart, Thibaut wrote:

> Hello, 
> 
> you need to use 'pop(x) <- ...' to change or set population information; for instance, using simulated data:
> 
>> x <- glSim(10,100)
>> pop(x)
> [1] A A A A A B B B B B
> Levels: A B
>> pop(x) <- rep(1:2, c(2,8))
>> pop(x)
> [1] 1 1 2 2 2 2 2 2 2 2
> Levels: 1 2
> 
> Cheers
> 
> Thibaut
> 
> 
> ________________________________________
> From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Tom Devitt [tommydevitt at gmail.com]
> Sent: 24 August 2012 13:25
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: [adegenet-forum] pop argument
> 
> Could someone please help me understand how to include population information using the pop argument for a genlight object? I've used the read.DNA argument to input my data (FASTA format) and then the fasta2genlight argument to extract SNPs. I don't know how to specify individual population assignments using the pop argument. Thanks for your help.
> 
> (Sorry if this is a repost - I tried sending this message a couple days ago, but am not sure it posted to the forum.)
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