I performed an association analysis with dosage data (.gen and .fam files) with PLINK 1.9 using imputated data and got back the association p-value for each SNP. Now, I want to do another association test with the same data, but using the SNP with the strongest association signal as a covariate (a conditional test).
The problem is that when i try to use the --condition option, a message appears saying "--dosage doesn't allow the conditional option".
Has anybody had the same problem? Any possible solutions or help are extremely welcome, since I'm breaking my head over here.
Type of data that I have:
SNP Position A1 A2 ProbA1A1_Subject1 ProbA1A2_Subject1 ProbA2A2_Subject1... for 5000 subjects