Hi,
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 files 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?
Thanks
•
written
by
bsmith030465
You could:
1) Change the affected status in the fam file. Smaller file, less steps.
or
2) Use the option --pheno to use an alternate phenotype.
•
written
by
Maxime Lamontagne
Yes, I could change the status in the fam file, but the old status would still remain in the bed file. Won't that be problematic for downstream analysis?
•
written
by
bsmith030465
No status in the bed file.
You can simply use the following code to get plink bed files with new phenotype:
plink --bfile PlinkBed --pheno replacementPhenotypes --make-bed --out PlinkBedWithPheno
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ok, thanks! That simplifies my job considerably!!