Feature request: dominance deviation testing and improved recessive+dominance tests

[samuelejones]

I understand that REGENIE has --test flag where you can specify "recessive" or "dominant", but I was wondering if there are any future plans to improve these. Specifically:

1. Dominance deviation testing (as in PLINK) where deviation from additivity is tested in addition to additive effect
2. Ability to perform multiple tests in one run, with multiple lines output per variant (one line per test) like in the interaction analyses, as currently --test can only take one modifier so can only perform one test (additive/recessive/dominance) at a time
3. Automatic allele flipping for recessive and dominance tests, as currently REGENIE will just use the alt allele, which is typically the minor allele in most large-scale datasets, but not always. The recessive and dominance test statistics are meaningless when the major allele is tested so REGENIE could force the minor allele to be the effect allele when recessive and/or dominance tests are run.

Any thoughts would be appreciated!

Thanks again for continuing to maintain REGENIE!

[joellembatchou]

Hi,

These are all great suggestions that we have already noted as potential enhancements but currently don't have bandwidth to work on implementing [ note that (3) could be addressed by forcing REF allele in the genotype file to be the major one, e.g. using --maj-ref in PLINK2 ].

Cheers,
Joelle