Hello, I am attempting to obtain covariates for my samples. Unfortunately, the original fam file I QCd on does not have the phenotypes listed. I did however, make a txt file updated with the fid, Ids and phenotype list we just acquired. I attempted to receive covariates using these files and this script in plink, thinking that it'll acquire the phenotype columns from my pheno txt file:
plink --bfile MAP_data6 --covar covar_mds_MAP_data6_Pr.txt --pheno phenoPRS6_widFID.txt --pheno-name HC,MDD,PTSD,Bipolar --linear hide-covar --out MAP_data6_logistic_results
However, this error came:
Error: --pheno-name column not found.
Here's an example of the first few lines of my pheno txt file (not formatted correctly here, but hopefully you get the point):
FID IID HC MDD PTSD Bipolar
82 PB001 MDD
3 PB005 MDD
17 PB006 MDD
Question: is it possible to run this covariate plink script using a non-phenotype fam file (all -9's are listed for phenotype), with an updated phenotype txt file?
If not, how can I do this without directly editing my .fam file. Or perhaps there is an easy way to update my fam file with phenotypes?
Thanks!
