addOxford <- function(chr) { 
  res <- subset(a12, chrom==chr)
  ox <- read.table(paste("chr",chr,"_rates.txt",sep=""),h=T)
  oxinterp <- approx(ox9$Position, ox9$Ox.cM, res$build35)
  res$Ox.cM <- oxinterp$y
}

affy1 <- read.delim("~/Genetics/Affy/affy_50K_HindIII.dat", sep="\t", head=FALSE)
affy2 <- read.delim("~/Genetics/Affy/affy_50K_XbaI.dat", sep="\t", head=FALSE)
a12 <- rbind(affy1, affy2)
rm(affy1, affy2)
names(a12) <- c("name2", "name1", "chrom", "build35", "alleleA","alleleB","European","African","Asian")
a12$chrom <- factor(a12$chrom, levels=c(as.character(1:22),"X",""))
a12 <- a12[order(a12$chrom, a12$build35), c(2,1,seq(3, ncol(a12))), ]
a12$name1 <- as.character(a9$name1)
a12$name2 <- as.character(a9$name2)
a12$name1[a9$name1==""] <- a9$name2[a9$name1==""]

for (chr in levels(a12$chrom)) {
  write.table(addOxford(chr), 
              paste("Affy",chr,".dat",sep=""), row.names=FALSE, quote=FALSE, na=".")
}