agtc <- function(a1,a2,b1,b2){
sig <- rep(1,length(a1))
for(i in 1:length(a1)){
if((is.na(a1[i]))||(is.na(a2[i]))||(is.na(b1[i]))||(is.na(b2[i]))){
sig[i] <- 0
}
else if((a1[i]==b1[i])&(a2[i]==b2[i])){
sig[i] <- 1
}else if((a1[i]==b2[i])&(a2[i]==b1[i])){
sig[i] <- -1
}
else{
if(b1[i]=="A"){temp1 <- "T"}
if(b1[i]=="T"){temp1 <- "A"}
if(b1[i]=="G"){temp1 <- "C"}
if(b1[i]=="C"){temp1 <- "G"}
if(b2[i]=="A"){temp2 <- "T"}
if(b2[i]=="T"){temp2 <- "A"}
if(b2[i]=="G"){temp2 <- "C"}
if(b2[i]=="C"){temp2 <- "G"}
if((a1[i]==temp1)&(a2[i]==temp2)){
sig[i] <- 1
}else if((a1[i]==temp2)&(a2[i]==temp1)){
sig[i] <- -1
}else{ sig[i] <- 0}
}
# if(i %% 10000==0){
# print(i)
# }
}
return(sig)
}
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