load(file="SubPopCorMat.Rda")
load(file="DenisovaMat.Rda")
load(file="NeanderMat.Rda")
load(file="PopulationMat.Rda")

sink(file = "CorPopCorRes.txt", append = FALSE)

names1=c("AFR","AMR","ASN","EUR")
names=c("AFRICAN","AD MIX AMERICAN","ASIAN","EUROPEAN")

  print("###############################")
  print(paste("####DENISOVA###########",sep=""))
  print("###############################")
  

for (pop in 6:9) {
# pop <- 9 #6 = "AFR" 7= "AMR" 8 = "ASN" 9 = "EUR"

  print("###############################")
  print(paste("####",names[pop-5],"####DENISOVA###########",sep=""))
  print("###############################")
  

t <- cor.test(PopulationMat[,pop],DenisovaMat[,12],method ="pearson")
print(t)
print(paste("==========",t$p.value,"=============",sep=""))

t <- cor.test(PopulationMat[,pop],DenisovaMat[,12],method ="spearman")
print(t)
print(paste("==========",t$p.value,"=============",sep=""))

thres1 <- 0.2
thres2 <- 0.3
L <- length(PopulationMat[,pop])

pa <- which(PopulationMat[,pop]>thres1)
pb <- which(DenisovaMat[,12]>thres2)


ab <- intersect(pa,pb) 


lab <- length(ab)
la <- length(pa)
lb <- length(pb)

laB <- la-lab
lAb <- lb-lab
lAB <- L - lab - laB - lAb

conf <- matrix(c(lab,laB,lAb,lAB),nrow=2,ncol=2)
t <- fisher.test(conf)
print(t)
print(paste("==========",t$p.value,"=============",sep=""))
  print("###############################")
}



#########################################################

#########################################################

#########################################################


#########################################################


#########################################################



names1=c("AFR","AMR","ASN","EUR")
names=c("AFRICAN","AD MIX AMERICAN","ASIAN","EUROPEAN")

  print("###############################")
  print(paste("####NEANDERTAL###########",sep=""))
  print("###############################")

for (pop in 6:9) {
# pop <- 9 #6 = "AFR" 7= "AMR" 8 = "ASN" 9 = "EUR"

  print("###############################")
  print(paste("####",names[pop-5],"####NEANDERTAL###########",sep=""))
  print("###############################")
  

t <- cor.test(PopulationMat[,pop],NeanderMat[,12],method ="pearson")
print(t)
print(paste("==========",t$p.value,"=============",sep=""))

t <- cor.test(PopulationMat[,pop],NeanderMat[,12],method ="spearman")
print(t)
print(paste("==========",t$p.value,"=============",sep=""))


thres1 <- 0.2
thres2 <- 0.3
L <- length(PopulationMat[,pop])

pa <- which(PopulationMat[,pop]>thres1)
pb <- which(NeanderMat[,12]>thres2)


ab <- intersect(pa,pb) 


lab <- length(ab)
la <- length(pa)
lb <- length(pb)

laB <- la-lab
lAb <- lb-lab
lAB <- L - lab - laB - lAb

conf <- matrix(c(lab,laB,lAb,lAB),nrow=2,ncol=2)
t <- fisher.test(conf)
print(t)
print(paste("==========",t$p.value,"=============",sep=""))
  print("###############################")
}





#########################################################

###############################################################

  print("###############################")
  print(paste("####DENISOVA 2###########",sep=""))
  print("###############################")
  
for (pop in 6:9) {
# pop <- 9 #6 = "AFR" 7= "AMR" 8 = "ASN" 9 = "EUR"

  print("###############################")
  print(paste("####",names[pop-5],"####DENISOVA 2###########",sep=""))
  print("###############################")
  
thres1 <- 0.2
thres2 <- 0.5
L <- length(PopulationMat[,pop])

pa <- which(PopulationMat[,pop]>thres1)
pb <- which(DenisovaMat[,12]>thres2)


ab <- intersect(pa,pb) 


lab <- length(ab)
la <- length(pa)
lb <- length(pb)

laB <- la-lab
lAb <- lb-lab
lAB <- L - lab - laB - lAb

conf <- matrix(c(lab,laB,lAb,lAB),nrow=2,ncol=2)
t <- fisher.test(conf)
print(t)
print(paste("==========",t$p.value,"=============",sep=""))
  print("###############################")
}


  print("###############################")
  print(paste("####DENISOVA 3###########",sep=""))
  print("###############################")

for (pop in 6:9) {
# pop <- 9 #6 = "AFR" 7= "AMR" 8 = "ASN" 9 = "EUR"

  print("###############################")
  print(paste("####",names[pop-5],"####DENISOVA 3###########",sep=""))
  print("###############################")
  
thres1 <- 0.4
thres2 <- 0.5
L <- length(PopulationMat[,pop])

pa <- which(PopulationMat[,pop]>thres1)
pb <- which(DenisovaMat[,12]>thres2)


ab <- intersect(pa,pb) 


lab <- length(ab)
la <- length(pa)
lb <- length(pb)

laB <- la-lab
lAb <- lb-lab
lAB <- L - lab - laB - lAb

conf <- matrix(c(lab,laB,lAb,lAB),nrow=2,ncol=2)
t <- fisher.test(conf)
print(t)
print(paste("==========",t$p.value,"=============",sep=""))
  print("###############################")
}




################################################################

###############################################################

###############################################################

###############################################################

###############################################################

##############################################################


###SSSSSSSSSSSSSS

  print("###############################")
  print("###############################")
  print("###############################")
  print("###############################")
  print("###############################")
  print("###############################")
  print("###############################")
  print("###############################")
  print("###############################")
  print("###############################")
  print("###############################")
  print("###############################")


names1 <- c("ASW","CEU","CEUKOR","CHB","CHS","CLM","FIN","GBR","IBS","JPT","KOR","KORdup","LWK","MXL","PUR","TSI","YRI")

names=c("HapMapAfricans", "CEPHEuropean", "mixKoreanCEU", "HanChineseBeijing", "HanChineseSouth", "Colombian", "HapMapFinnish", "British", "Iberian", "Japanese", "KOREAN", "KOREANfamily", "Luhya", "MapMapMexican", "PuertoRican", "Toscan", "Yoruba") 


  print("###############################")
  print(paste("####DENISOVA###########",sep=""))
  print("###############################")
  

for (pop in 6:20) {


  print("###############################")
  print(paste("####",names[pop-5],"####DENISOVA###########",sep=""))
  print("###############################")
  

t <- cor.test(SubPopCorMat[,pop],DenisovaMat[,12],method ="pearson")
print(t)
print(paste("==========",t$p.value,"=============",sep=""))

t <- cor.test(SubPopCorMat[,pop],DenisovaMat[,12],method ="spearman")
print(t)
print(paste("==========",t$p.value,"=============",sep=""))

thres1 <- 0.2
thres2 <- 0.3
L <- length(SubPopCorMat[,pop])

pa <- which(SubPopCorMat[,pop]>thres1)
pb <- which(DenisovaMat[,12]>thres2)


ab <- intersect(pa,pb) 


lab <- length(ab)
la <- length(pa)
lb <- length(pb)

laB <- la-lab
lAb <- lb-lab
lAB <- L - lab - laB - lAb

conf <- matrix(c(lab,laB,lAb,lAB),nrow=2,ncol=2)
t <- fisher.test(conf)
print(t)
print(paste("==========",t$p.value,"=============",sep=""))
  print("###############################")
}



#########################################################

#########################################################

#########################################################


#########################################################


#########################################################


names1 <- c("ASW","CEU","CEUKOR","CHB","CHS","CLM","FIN","GBR","IBS","JPT","KOR","KORdup","LWK","MXL","PUR","TSI","YRI")

names=c("HapMapAfricans", "CEPHEuropean", "mixKoreanCEU", "HanChineseBeijing", "HanChineseSouth", "Colombian", "HapMapFinnish", "British", "Iberian", "Japanese", "KOREAN", "KOREANfamily", "Luhya", "MapMapMexican", "PuertoRican", "Toscan", "Yoruba") 



  print("###############################")
  print(paste("####NEANDERTAL###########",sep=""))
  print("###############################")

for (pop in 6:20) {


  print("###############################")
  print(paste("####",names[pop-5],"####NEANDERTAL###########",sep=""))
  print("###############################")
  

t <- cor.test(SubPopCorMat[,pop],NeanderMat[,12],method ="pearson")
print(t)
print(paste("==========",t$p.value,"=============",sep=""))

t <- cor.test(SubPopCorMat[,pop],NeanderMat[,12],method ="spearman")
print(t)
print(paste("==========",t$p.value,"=============",sep=""))


thres1 <- 0.2
thres2 <- 0.3
L <- length(SubPopCorMat[,pop])

pa <- which(SubPopCorMat[,pop]>thres1)
pb <- which(NeanderMat[,12]>thres2)


ab <- intersect(pa,pb) 


lab <- length(ab)
la <- length(pa)
lb <- length(pb)

laB <- la-lab
lAb <- lb-lab
lAB <- L - lab - laB - lAb

conf <- matrix(c(lab,laB,lAb,lAB),nrow=2,ncol=2)
t <- fisher.test(conf)
print(t)
print(paste("==========",t$p.value,"=============",sep=""))
  print("###############################")
}





#########################################################

###############################################################

  print("###############################")
  print(paste("####DENISOVA 2###########",sep=""))
  print("###############################")
  
for (pop in 6:20) {


  print("###############################")
  print(paste("####",names[pop-5],"####DENISOVA 2###########",sep=""))
  print("###############################")
  
thres1 <- 0.2
thres2 <- 0.5
L <- length(SubPopCorMat[,pop])

pa <- which(SubPopCorMat[,pop]>thres1)
pb <- which(DenisovaMat[,12]>thres2)


ab <- intersect(pa,pb) 


lab <- length(ab)
la <- length(pa)
lb <- length(pb)

laB <- la-lab
lAb <- lb-lab
lAB <- L - lab - laB - lAb

conf <- matrix(c(lab,laB,lAb,lAB),nrow=2,ncol=2)
t <- fisher.test(conf)
print(t)
print(paste("==========",t$p.value,"=============",sep=""))
  print("###############################")
}


  print("###############################")
  print(paste("####DENISOVA 3###########",sep=""))
  print("###############################")

for (pop in 6:20) {


  print("###############################")
  print(paste("####",names[pop-5],"####DENISOVA 3###########",sep=""))
  print("###############################")
  
thres1 <- 0.4
thres2 <- 0.5
L <- length(SubPopCorMat[,pop])

pa <- which(SubPopCorMat[,pop]>thres1)
pb <- which(DenisovaMat[,12]>thres2)


ab <- intersect(pa,pb) 


lab <- length(ab)
la <- length(pa)
lb <- length(pb)

laB <- la-lab
lAb <- lb-lab
lAB <- L - lab - laB - lAb

conf <- matrix(c(lab,laB,lAb,lAB),nrow=2,ncol=2)
t <- fisher.test(conf)
print(t)
print(paste("==========",t$p.value,"=============",sep=""))
  print("###############################")
}







sink()