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?

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