I need to change the affection status in my PLINK files (data1.bed, data1.bim, data1.fam) to '2' for all samples. To do this, I was thinking of:
1. Convert bed to ped using:
plink --bfile data1 --recode --tab --out data2
2. Copy data1.fam as data2.fam
3. Change the 6th column of both the data2.fam and data2.ped file so that the new affection status is '2' for everything
4. Convert the modified ped file back to bed using:
plink --ped data2.ped --map data2.map
Do these steps look complete and correct for what I am trying to do?