R语言生成plink测试数据

1、

result1 <- data.frame(1:100)

for (i in 1:10) {
  temp1 <- sample(c("A", "C", "G", "T"), 2, replace = F)
  temp2 <- sample(c(temp1[1], temp1[2]), 100, replace = T)
  result1 <- cbind(result1, temp2)
}
result1 <- result1[,-1]

ped <- data.frame()
for (i in 1:(nrow(result1)/2)) {
  vec <- vector()
  for (j in 1:ncol(result1)) {
    vec <- c(vec, result1[2 * i -1, j], result1[2 * i, j])
  }
  ped <- rbind(ped, vec)
}
colnames(ped) <- paste0("v", 1:ncol(ped))

dim(ped)
fid <- rep("breed1", nrow(ped))
iid <- 1:nrow(ped)
fa <- rep("0", nrow(ped))
ma <- rep("0", nrow(ped))
sex <- rep("0", nrow(ped))
phe <- rep("-9", nrow(ped))
ped <- cbind(fid, iid, fa, ma, sex, phe, ped)

chr <- rep(1, (ncol(ped) - 6)/2)
snp <- paste0("snp", 1:length(chr))
dis <- rep(0, length(chr))
pos <- 1:length(chr)
map <- data.frame(chr, snp, dis, pos)
ped
map
write.table(ped, "test.ped", row.names = F, col.names = F, quote = F, sep = "\t")
write.table(map, "test.map", row.names = F, col.names = F, quote = F, sep = "\t")

 

 

 

 

2、plink验证

root@PC1:/home/test# ls
test.map  test.ped
root@PC1:/home/test# plink --file test --recode --out 111