plink 軟體中 --set-missing-var-ids 命令
阿新 • • 發佈：2021-12-14
plink中--set-missing-var-ids 用於對缺失snpID的snp設定名稱
1、測試資料
root@PC1:/home/test# ls outcome.map outcome.ped root@PC1:/home/test# cat outcome.ped DOR 1 0 0 0 -9 G G C C G G G G A G A A G G G C A G A A DOR 2 0 0 0 -9 G G G C G G G G G G A A A G C C A G A A DOR3 0 0 0 -9 G G C C G G G G G G A A A G G C G G A A DOR 4 0 0 0 -9 G G C C G G G G G G A A G G G G G G A A DOR 5 0 0 0 -9 G G C C G G G G G G A A A G G C G G A A DOR6 0 0 0 -9 G G C C G G G G G G A A A A C C G G A A root@PC1:/home/test# cat outcome.map ## 一共10個snp， 後5個snpID缺失， 為“.” 1 s64199.1 0 55910 1 OAR19_64675012.1 0 85204 1 OAR19_64715327.1 0 1229481 OAR19_64803054.1 0 203750 1 DU281551_498.1 0 312707 1 . 0 356863 1 . 0 400518 1 . 0 487423 1 . 0 578716 1 . 0 639876
2、利用 plink--set-missing-var-ids 增加唯一ID ，--set-missing-var-ids後使用@和#
root@PC1:/home/test# plink --file outcome --set-missing-var-ids @:# --recode tab --out result root@PC1:/home/test# ls outcome.map outcome.ped result.log result.map result.nosex result.ped root@PC1:/home/test# cat result.map ## 將第1列和第2列合併為snpID 1 s64199.1 0 55910 1 OAR19_64675012.1 0 85204 1 OAR19_64715327.1 0 122948 1 OAR19_64803054.1 0 203750 1 DU281551_498.1 0 312707 1 1:356863 0 356863 1 1:400518 0 400518 1 1:487423 0 487423 1 1:578716 0 578716 1 1:639876 0 639876
3、可以增加其他修飾
root@PC1:/home/test# plink --file outcome --set-missing-var-ids head@_#end --recode tab --out result2 root@PC1:/home/test# ls outcome.map outcome.ped result2.log result2.map result2.nosex result2.ped result.log result.map result.nosex result.ped root@PC1:/home/test# cat result2.map ## @和#是必須的，其餘可選 1 s64199.1 0 55910 1 OAR19_64675012.1 0 85204 1 OAR19_64715327.1 0 122948 1 OAR19_64803054.1 0 203750 1 DU281551_498.1 0 312707 1 head1_356863end 0 356863 1 head1_400518end 0 400518 1 head1_487423end 0 487423 1 head1_578716end 0 578716 1 head1_639876end 0 639876
4、shell實現
（2）
root@PC1:/home/test# cat outcome.map 1 s64199.1 0 55910 1 OAR19_64675012.1 0 85204 1 OAR19_64715327.1 0 122948 1 OAR19_64803054.1 0 203750 1 DU281551_498.1 0 312707 1 . 0 356863 1 . 0 400518 1 . 0 487423 1 . 0 578716 1 . 0 639876 root@PC1:/home/test# awk '{OFS = "\t"}{if($2 ~ /^\./) {print $1, $1":"$4, $3,$4} else {print $0}}' outcome.map 1 s64199.1 0 55910 1 OAR19_64675012.1 0 85204 1 OAR19_64715327.1 0 122948 1 OAR19_64803054.1 0 203750 1 DU281551_498.1 0 312707 1 1:356863 0 356863 1 1:400518 0 400518 1 1:487423 0 487423 1 1:578716 0 578716 1 1:639876 0 639876
（2）、
root@PC1:/home/test# cat outcome.map 1 s64199.1 0 55910 1 OAR19_64675012.1 0 85204 1 OAR19_64715327.1 0 122948 1 OAR19_64803054.1 0 203750 1 DU281551_498.1 0 312707 1 . 0 356863 1 . 0 400518 1 . 0 487423 1 . 0 578716 1 . 0 639876 root@PC1:/home/test# awk '{OFS = "\t"}{if($2 == ".") {print $1, $1":"$4, $3, $4} else {print $0}}' outcome.map 1 s64199.1 0 55910 1 OAR19_64675012.1 0 85204 1 OAR19_64715327.1 0 122948 1 OAR19_64803054.1 0 203750 1 DU281551_498.1 0 312707 1 1:356863 0 356863 1 1:400518 0 400518 1 1:487423 0 487423 1 1:578716 0 578716 1 1:639876 0 639876
5、R實現
dat <- read.table("outcome.map", header = F) dat for (i in 1:nrow(dat)) { ## 利用迴圈判斷實現 if (dat[i,2] == ".") { dat[i,2] = paste(dat[i,1], dat[i,4], sep = ":") } } dat