How to add strata information to a genind - r

Question

I have created a genind object from a table containing SNPs information.
I need to insert population information into this genind.
I know which individuals (which are identified by numbers) should go into each population.
How do I pick the correct individuals and place them into separate populations?

Answer 1

It's always helpful to make a reproducible example when asking a question.
First, loading the necessary library (pretty sure its adegenet)
library(adegenet)
Making some fake data by first getting a vector of alleles
alleles <- paste0("0",1:4)
Setting number of loci, individuals per population, and the number of populations
nloci <- 10
nind <- 10
npops <- 2
Using a for loop to make the fake dataset
i <- NULL
out <- NULL
for(i in 1:npops){
#there are nind*nloci genotypes in each population
#make a
gts <- replicate(n = nind*nloci,
expr = paste0(sample(x = alleles,size = 1,replace = T),
sample(x = alleles,size = 1,replace = T)))
gts <- as.data.frame(matrix(data = gts,
nrow = nind, ncol = nloci, byrow = T))
#making generic locus colnames()
colnames(gts) <- paste("locus_",1:nloci)
out <- rbind(out,gts)
} #end of for loop
head(out)
Now converting that data.frame into a genind
obj <- df2genind(out, ploidy=2, ncode=2)
obj
Note that the row.names() are considered individual IDs
Now for setting the populations, note its empty right now
obj#pop
You just need a vector that represents the populations corresponding to each individual.
Option 1
If your individual IDs are clustered by population (e.g. 1-10 are from pop1 and 11-20 are from pop2), then something like this should work
pops<- paste0("pop",1:npops)
Set the populations using that vector, make sure it's a factor
obj#pop <- as.factor(rep(pops,each=nind))
obj#pop
Option 2
If the original data.frame (table) that contained your SNP information also contained population information, you could use that as your vector
e.g. If out looked like this
out$pops <- sample(x = pops,size = nrow(out),replace = T)
head(out)
Then do could use that column as your vector
obj#pop <- as.factor(out$pops)
obj#pop
Option 3
Alternatively, if you had another table that enabled you to identify which individuals corresponded to which population, then you use that information. It assumes that the second table (data.frame) is the same number of rows as out
Here is an example second table
df <- data.frame(pops = rep(pops,each=nind),
id = sample(x = 1:nrow(out),size = nrow(out),replace = F))
head(df)
Note that the IDs are not in order, but they were in out and therefore are in the obj, so df needs to be ordered by df$id
df <- df[order(df$id),]
head(df)
After they are in the correct order
obj#pop <- as.factor(df$pops)
obj#pop