19_halibut_stamp_FST

library(vcfR)
library(adegenet)
library(StAMPP)
library(rsed)
library(dplyr)
setwd("~/Desktop/Projects/Halibut_FinalRAD/")
system("~/Desktop/Software/plink_mac_20200219/plink --file Halibut_finalgenome_mindp15_24chrom_ming90_HWE_noWF_allENV  --recode vcf --chr-set 24 --within Gulfnogulf.txt --out Halibut_finalgenome_mindp15_24chrom_ming90_HWE_noWF_allENV")

##2.1 Read vcf file into into R
vcf<-read.vcfR("Halibut_finalgenome_mindp15_24chrom_ming90_HWE_noWF_allENV.vcf", verbose = FALSE)
##2.2 Convert vcf into genlight object
x <- vcfR2genlight(vcf)


FAM <- read.delim("Halibut_finalgenome_mindp15_24chrom_ming90_HWE_noWF_allENV.fam", stringsAsFactors = F, header = F, sep = "")
Metadata <- read.delim("Metadata_Halibut_ENV_noNAnoWF.txt", header = T, stringsAsFactors = F)
ID <- FAM[1]
colnames(ID)[1] <- "ID"
Metadata_sorted <- inner_join(ID, Metadata)
sample <- ID
pop.names <- Metadata_sorted$Region
Gulf_FST_list <- read.delim("Gulfnogulf.txt", header = F)
colnames(Gulf_FST_list) <- c("ID", "ID_also", "Group")
Metadata_sorted <- inner_join(Metadata_sorted, Gulf_FST_list)
Metadata_sorted$Group <- as.factor(Metadata_sorted$Group)
x@ind.names <- Metadata_sorted$ID
x@pop <- as.factor(Metadata_sorted$Group)
geno <- stamppConvert(x, type = "genlight") 

FST_WC <- stamppFst(geno = geno, nboots = 500, nclusters = 20)