[adegenet-forum] Genind object inquiry

[Roman Luštrik]

If I understand correctly, you can use the assign function for ?pop, e.g. 

data(H3N2) 

nInd(H3N2) 
# [1] 1903 

pop(H3N2) 
# NULL 

# will make each individual in its own population 
pop(H3N2) <- 1:1903 

# see 
pop(H3N2) 

Cheers, 
Roman 
---- 
In god we trust, all others bring data. 


From: "Felipe Hernández" <fhernandeu at uc.cl> 
To: adegenet-forum at lists.r-forge.r-project.org 
Sent: Saturday, October 15, 2016 7:42:46 PM 
Subject: [adegenet-forum] Genind object inquiry 

Good afternoon, 
Perhaps this's a pretty basic question, but I have been struggling in order to set the populations which my individuals belong to in my microsat dataset. In other words, I don't understand how to set the slot 'pop' when I create a genind object from a csv file that contains all my genetic data. For example, should I include in my matrix a column containing the population codes which my individuals belong to (beside all my locus columns)? Or, should I just include my loci info? I realised if I include the column with the population codes in my genind object, this is also considered as a locus, and surely, this's no correct. I assume that solving this issue, I may appropriately transform my genind object to a genpop object, which is my next goal to continue with my analyses. Thank you in advance for your valuable input, thanks! 

Regards, 
Felipe 

-- 
Felipe Hernández 
Médico Veterinario (DVM), MSc. 
PhD. Candidate 
Interdisciplinary Ecology Program 
School of Natural Resources and Environment 
Wildlife Ecology and Conservation Department 
University of Florida 

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