vcf <- read.table("/seppdata/sepp/linkage/neanderthal_denisova/T_hg19_1000g.Genotypes.vcf",sep="\t") hg19 <- read.table("/seppdata/sepp/linkage/neanderthal_denisova/hg191000.bed",sep="\t") hg19M <- paste(as.character(hg19[,1]),as.character(as.numeric(hg19[,2])),sep="") vcfM <- paste("chr",as.character(vcf[,1]),as.character(as.numeric(vcf[,2])),sep="") mm <- match(vcfM,hg19M,nomatch=0) ma <- which(mm>0) adds <- vcf[ma,5] refs <- vcf[ma,4] pos <- hg19[mm[ma],4] l <- length(hg19[,4]) ad1 <- rep("-",l) ref1 <- rep("-",l) ad1[mm[ma]] <- as.character(adds) ref1[mm[ma]] <- as.character(refs) denisovaHg19 <- cbind(hg19,ref1,ad1) denisovaHg19[1:100,] save(denisovaHg19,file="denisovaHg19.Rda") chr1 <- which(denisovaHg19$V1=="chr1") denisovaHg19Chr1 <- denisovaHg19[chr1,] save(denisovaHg19Chr1,file="denisovaHg19Chr1.Rda") #################################################################### hg18 <- read.table("/seppdata/sepp/linkage/neanderthal_denisova/hg181000.bed",sep="\t") hg19 <- read.table("/seppdata/sepp/linkage/neanderthal_denisova/hg191000.bed",sep="\t") vcf <- read.table("/seppdata/sepp/linkage/neanderthal_denisova/NeandertalGenotypes.vcf",sep="\t") hg18M <- paste(as.character(hg18[,1]),as.character(as.numeric(hg18[,2])),sep="") vcfM <- paste(as.character(vcf[,1]),as.character(as.numeric(vcf[,2])),sep="") mm <- match(vcfM,hg18M,nomatch=0) ma <- which(mm>0) adds <- vcf[ma,5] refs <- vcf[ma,4] pos <- hg18[mm[ma],4] mp <- match(pos,hg19[,4],nomatch=0) mpa <- which(mp>0) adds <- adds[mpa] refs <- refs[mpa] mp <- mp[mpa] l <- length(hg19[,4]) ad1 <- rep("-",l) ref1 <- rep("-",l) ad1[mp] <- as.character(adds) ref1[mp] <- as.character(refs) neanderHg19 <- cbind(hg19,ref1,ad1) save(neanderHg19,file="neanderHg19.Rda") chr1 <- which(neanderHg19$V1=="chr1") neanderHg19Chr1 <- neanderHg19[chr1,] save(neanderHg19Chr1,file="neanderHg19Chr1.Rda")