[GenABEL-dev] Creating a complex coxph model

[L.C. Karssen]

Dear Jeff,

Thanks for contacting us on the mailing list.


On 04-05-15 11:17, Jeff Alstott wrote:
> Hello,
> 
> I am trying to use DatABEL do run a coxph model.

I guess you mean ProbABEL, right? DatABEL is only used to store and
efficiently access large data sets. ProbABLE implements the Cox PH model.

>  I am not using DatABEL
> for its intended purpose, of running a straightforward model in which
> every column is a SNP that will be put into the model. Instead, I need
> to do something more complex. I would like to do something like this:
> 
> Surv(38579, column1) ~ column2 + column3 + column2*column3 + strata(column4)
> 

So, from your follow-up mail:

Surv(rep(1, n_rows), column1) ~ column2 + column3 + column2*column3 +
strata(column4)

Sounds interesting. One thing I didn't really understand from your
e-mail: do the 4 columns contain SNP data? Or simple another
(non-genetic) large data set.

Currently we don't have a strata()-like function in ProbABEL, but maybe
you could get around that by doing some recoding.


Best regards,

Lennart.

> Is this possible in DatABEL? This is actually just setting up the form
> to do a conditional logistic regression, which if set up correctly is
> equivalent to a Cox proportional hazards model. The survival package
> implements this nicely. I just have far too large of a dataset and want
> DatABEL to help me run the regression.
> 
> 
> survival's clogit:
> https://stat.ethz.ch/R-manual/R-devel/library/survival/html/clogit.html
> 
> 
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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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