How to calculate Fst of each SNP between populations using PopGenome

Question

[grandlee]

Hello everyone,

I'd like to calculate Fst of each SNP between population using PopGenome. Finally, I'd like to detect high-Fst SNPs and plot Fst of each SNP like manhattan plot.

In my case, there are 3 bacteria populations. I'd like to calculate Fst of each SNP such that [Pop1 vs other populations(Pop2 and Pop3)], [Pop2 vs others(Pop1 and Pop3)], [Pop3 vs others(Pop1 and Pop2)].

At first, I defined 3 populations.

x <- readData("VCF", format="VCF", gffpath="GFF")
Pop1 <- as.character(read.csv("pop1.csv")[[1]])
Pop2 <- as.character(read.csv("pop2.csv")[[1]])
Pop3 <- as.character(read.csv("pop3.csv")[[1]])
x <- set.populations(x, list(Pop1, Pop2, Pop3))
x@populations #check

Then, to verify synonymous and non-synonymous SNPs,

x <- set.synnonsyn(x, ref.chr="referene.fasta")

To calculate Fst of each SNPs,

x <- detail.stats(x, site.FST=TRUE)
[e-mail]@siteFST

But, I don't know how to set population information.

Could you please tell me how to?

Regards,