[GenABEL-dev] ProbABEL: mmscore and interaction

[Maksim Struchalin]

Hi Lennart,

If ProbABEL is using the same 'two steps score test' as it was in the 
first version (section 'Two-step score test for association' in ProbABEL 
paper http://www.biomedcentral.com/1471-2105/11/134) then, I guess, the 
GxE term can be included in the model and run in mmscore. It only should 
be assured that the interaction term goes to the second step (run the 
model trait_residuals ~ snp + snp*E in mmscore). Otherwise, it may 
results in false positives.

Actually, in the first paragraph of section 'Two-step score test for 
association' of ProbABEL paper, it is written that "design matrix may 
include not only the main SNP effect, but e.g. SNP by environment 
interaction terms". So, I would include it and look what will happen.

P.S. IMHO it is interesting to run this scenario briefly in a small 
simulation study.

Best,
Maksim



On 17/10/2014 21:54, L.C. Karssen wrote:
> Dear list,
>
> There is a question on the forum [1] that I'm not sure how to answer.
> The user wants to run mmscore and test for interactions. There is
> nothing in ProbABEL that prevents her from doing that. However, in the
> manual we state:
>
> "Though technically --mmscore allows for inclusion of multiple
> covariates, these should be kept to minimum as this is a score test. We
> suggest that any covariates explaining an essential proportion of
> variance should be fit as part of GenABEL's polygenic procedure."
>
> Does this also apply for interactions between SNP and a covariate? If so
> we should produce an error message when both options are specified.
>
>
> What is the proper way to deal with interactions and mmscore?
>
>
> Best,
>
> Lennart.
>
>
> [1] http://forum.genabel.org/viewtopic.php?f=10&t=896
>
>
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