[adegenet-forum] assigning pop in genind object
t.jombart at imperial.ac.uk
Fri Feb 8 14:58:43 CET 2013
please have a look at the documentation, especially the vignette on basics (vignette("adegenet-basics")).
You want to use :
pop(hj) <- ...
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of takele taye [takele_taye at yahoo.com]
Sent: 08 February 2013 12:49
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] assigning pop in genind object
I converted my hj.str data into genind object using the read.structure function.
hj<- read.structure(file="hj.str", n.ind=747, n.loc=168344, onerowperind=TRUE, col.lab=1, col.pop=2, NA.char=-9, ask=FALSE)
My data contains two populations (represented by 1 & 2 in pop column of the hj.str data), the data was not sorted by population. How can I define the population of each individual in the genind object hj at pop.
I tried this one
pop_1 <- hj at pop==1
pop_2 <- hj at pop==2
However, this has clumped the entire population just into two dots instead of representing each individual in the PCA plot.
Any help is appreciated
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