PLINK won't allow me to replace the phenotype column in the .fam or .ped files using the --pheno command. The output reads phenotypes as missing and reports "0 phenotype values present after --pheno."
Current phenotypes are binary: HTA, CAD, OSA... Options are Case (2) or Control (1). Phenotypes are coded in tab separated .txt files.
PLINK Input: .ped
1 NJV 0 0 1 0
2 3SA 0 0 1 0
3 7SA 0 0 2 0
Input phenotype: .txt (Example CAD)
1 NJV 0 0 1 1
2 3SA 0 0 1 2
3 7SA 0 0 2 2
PLINK Output: .fam
1 NJV 0 0 1 -9
2 3SA 0 0 1 -9
3 7SA 0 0 2 -9
I processed my data with GenomeStudio and was able to perform QC and PCA in Plink. Available files in .ped, .bed, .vcf formats.
What could I do? If there's another program to deal with this (hopefully compatible with R). Or, is there a procedure in PLINK to work this out?
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written
by
sabrilo171 •
1 answer
Your phenotype file should have only FID, IID and Pheno columns as below. Here column first is FID, second IID and their is Pheno (1=Control and 2=Case).
cat phenotype.txt
1 NJV 1
2 3SA 2
3 7SA 2
After you prepare the phenotype file, you can update phenotype info in your plink files using following command-
plink --bfile your_data --pheno phenotype.txt --make-bed --out your_data_phenotype_updated
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