#Set working directory
setwd("~/Desktop/Analysis")
library(Rhh)

#Save MHC genotypes (from excel sheet) as a tab delimited txt file in working directory and delete header row
#Do the same for the Non-MHC genotypes (from excel sheet)

#Analyse MHC Genotypes
h <- mlh("MHC Genotypes.txt", "MHC-Hs.txt", "NA", 4) #Saves results in working directory
r <- h_cor("MHC Genotypes.txt", "0", 1000, "sh")
mean(r)
quantile(r, probs=c(0.025, 0.975))
hist(r)


#Analyse Non-MHC Genotypes
h <- mlh("Non-MHC Genotypes.txt", "Non-MHC-Hs.txt", "NA", 4) #Saves results in working directory
r <- h_cor("Non-MHC Genotypes.txt", "0", 1000, "sh")
mean(r)
quantile(r, probs=c(0.025, 0.975))
hist(r)


# Determine correlation between Hs at MHC vs Non-MHC loci
MHC <- read.table("MHC-Hs.txt", header = TRUE)
Non-MHC <- read.table("Non-MHC-Hs.txt", header = TRUE)
cor.test(MHC$SH, Non-MHC$SH, method = "spearman", continuity = FALSE, conf.level = 0.95)
library(RVAideMemoire)
library(vegan)
spearman.ci(MHC$SH, Non-MHC$SH, nrep = 1000, conf.level = 0.95)
plot(MHC$SH, Non-MHC$SH)