Hello, I would like tu run analysis using PLINK for SNPs but with recessive model as the default model used in logistic test is additive. could you please give me your advice. thanks a lot in advance PS: I tested the SNP using logistic regression test and 6 covariates but this time the reviewer asked for the same test but in recessive model instead of the default additive model
At the plink homepage there is a very nice and clear guideline for performing different genetic models:
From the homepage:
To specify a model assuming full dominance (or recessive) for the minor allele (i.e. rather than the 2 df model mentioned above), you can specify with either
the way of doing it is pretty well explained in plink web page (--logistic --recessive). However, the other question is whether it is wise to do so.
What will be the genotype frequency of you rare genotype under the recessive model. Especially as you are also including six covariates (are you sure they are all independent - at least a little bit).
I think that if you really need to get rid of a reviewer, you may also want to test the full model expressed with additive and dominance component, in order to see whether this dominance component is significant (showing deviation from additive).