I am currently using multinomial logistic regression to model disease outcome based on genetic haplotype. I've included 4 haplotypes in my model along with covariates as dependent variables. I've coded the values at each haplotype to correspond with the number of copies of that haplotype each individual is predicted to have and used the most common haplotype as the reference. In addition I've created a dummy value if the person does not have any copies of the haplotype. Unfortunately the dummy variable is affecting my model. Does anyone know of a way to set this value to zero (df=0) in the logistic model?
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