Covariates on non-phenotype fam file?
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7 months ago

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!

plink genotyping covariates • 267 views
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