1、R脚本
dir() dat <- read.table("outcome.ped") dat id <- dat[,2] dat <- dat[, -(1:6)] result <- data.frame() for (i in 1:nrow(dat)) { count = 0 for (j in 1:ncol(dat)) { if (dat[i,j] == 0) { count = count + 1 } } temp <- c(count/2,ncol(dat)/2, count/ncol(dat)) result <- rbind(result, temp) } result <- cbind(id, result) colnames(result)[2:4] <- c("misssite","totalsite","rate") result
2、plink验证
[root@centos79 test]# ls outcome.map outcome.ped result.txt test.sh [root@centos79 test]# plink --file outcome --missing --out verify > /dev/null; rm *.log *.nosex [root@centos79 test]# ls outcome.map outcome.ped result.txt test.sh verify.imiss verify.lmiss [root@centos79 test]# cat verify.imiss FID IID MISS_PHENO N_MISS N_GENO F_MISS DOR 1 Y 4 8 0.5 DOR 2 Y 4 8 0.5 DOR 3 Y 3 8 0.375 DOR 4 Y 2 8 0.25 DOR 5 Y 1 8 0.125 DOR 6 Y 1 8 0.125
