[GenABEL-dev] ProbABEL: mmscore and interaction

[L.C. Karssen]

Hi Maksim,



On 18-10-14 03:13, Maksim Struchalin wrote:
> 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)

Yes it does. Nothing was changed there.

>  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.
> 

Thanks! I'll have a look.

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


Good suggestion. I hope to have some time for that.


Best,

Lennart.

> 
> 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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> 
> 
> 
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-- 
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L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
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