ProbABEL - polytomous models?

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divarisk
Posts: 1
Joined: Tue Feb 08, 2011 7:34 pm

ProbABEL - polytomous models?

Postby divarisk » Tue Feb 08, 2011 7:54 pm

Hello all,
Very glad to see this group materialize and excited to join you all!
My question has to do with the implementation of polytomous/multinomial (or ordinal) logistic models for GWA applications using ProbABEL. Although not entirely familiar with the specifics of R, I am aware the the mlogit function of R can accommodate these models. Morris et al. Genet Epidemiol. 2010 present some background on this topic.
Are you aware of any way to link these via R code/script, or any other way around, so that running polytomous GWA analyses becomes feasible with ProbABEL?
Any insights or directions will be very helpful.
Thanks,
-Kimon

yurii
GenABEL developer
GenABEL developer
Posts: 263
Joined: Fri Jan 21, 2011 5:20 pm

Re: ProbABEL - polytomous models?

Postby yurii » Tue Feb 08, 2011 9:11 pm

We did not implement such models specifically in any of *ABELs.

My suggestion is to use 'apply2dfo' of DatABEL, which will allow you to run mlogit on every SNP in your data. It should do the job, though be prepared to spend hours to complete the GWAS.

To get familiar with apply2dfo, install DatABEL from CRAN, and try 'example(apply2dfo)' to see how that works.

If you manage to do that, everybody will appreciate if you post your syntax here!
Note that (Gen)ABELs are dynamically developing; while this post is intended to provide full information at the time of posting, please read on further posts, if any, as the topic may be updated with novel solutions at a later stage.

best regards,
Yurii


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