I'm working with a study where we have collected the subjects' genotypes for risk factors for a disease. These can be homozygous non-risk (e.g. AA), homozygous risk (e.g. TT) or heterozygous (e.g. AT) where that may have no risk or partial risk.
logistic regression: Does MarkerConcentration predict disease independently of the risk factors, or visa versa?
lm(Case ~ MarkerConcentration + Genotype1 + Genotype2)
linear regression: Can the risk factors affect marker concentration independently of disease state?
lm(MarkerConcentration ~ Case + Genotype1 + Genotype2)
In our analysis, we only include cases which homozygous risk or non-risk. and coding those as 1 and 0 respectively.
Would there be any value to treating these as ordinal variables with risk > non-risk?
Note that we do not have sufficient confidence in any estimate of relative risk to use that information
EDIT: I have rephrased the question to clarify that the genotype risk-factors are predictor variables.