Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
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4 weeks ago
F110152169 • 0

Hi,

I am new to PLINK and I am having trouble using one of the commands. I am trying to perform logistic regression analysis on several Ped and map files. Here is the command I put in:

plink --file TWBR10907-07_TWB2_QC --covar TWB2.0_2.6_2.txt --logistic --covar-name FID,IID,SEX,PARKISON --out logistic_results

TWB2.0_2.6_2.txt:
FID IID SEX PARKISON
TV2N_20203805G  TV2N_20203805G  1   0
TV23_20182701G  TV23_20182701G  1   0
TV29_20181602E  TV29_20181602E  1   0
TV23_20182809B  TV23_20182809B  2   0
TV23_20180107G  TV23_20180107G  2   0
TV2N_20203806G  TV2N_20203806G  2   0
TV23_20180108G  TV23_20180108G  1   0
TV29_20181603F  TV29_20181603F  1   0
TV21_20180301B  TV21_20180301B  1   0

I get back the following message and error:

283083 variants loaded from .bim file.
81236 people (25584 males, 55652 females) loaded from .fam.
81236 phenotype values loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Error: Missing --covar-name token in --covar file header line.

I've searched online and I can't find anything on this error. Can anyone please help me out?

Exia

PLINK GWAS SNP • 345 views
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Try: --covar-name SEX,PARKISON

FID and IID are Family ID and Individual ID, they are not covariates.

Side note, if PARKISON means "Parkinson's disease", then it is a typo.

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It's Parkinson's disease. How do I get the right order?

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