[GenABEL-dev] Robust Standard Errors for Cox Proportional Hazard Regression

[L.C. Karssen]

Dear Alisa,

Great to hear you have some time to spend on ProbABEL! Even more so
since you are willing to give the Cox regression module some much-needed
love.

In short, the status of Cox regression in ProbABEL is the following:
- In PA 0.2.0 Cox regression is disabled by default because it doesn't
work correctly (but it can be enabled easily). Looking back it seems
that it broke with the integration of the filevector/DatABEL code,
somewhere between the 0.1-3 and 0.1-9 releases.
- For those who want functional Cox regression (although not with
filevector data) I suggest to use PA 0.1-3. Recently we've implemented a
bugfix in that code base and we are almost ready to make that version
available to the public.

So, at the moment we have two code bases. Ideally we would like to get
the filevector problem solved in the PA 0.2.0 branch (the bugfix from
0.1-3 has also been implemented there). If you think you are up to it
you are more than welcome to see if you can fix the filevector problem
in 0.2.0!

If you want to focus more on the implementation of the weighted Cox
regression I guess it's easier to base your work on the 0.1-3-fixes code
where you can easily make test runs. Once it works you can forward-port
your improvements to the 0.2.0 branch.

Yurii, do you agree?


On the technical side of things: do you know how to work with
Subversion? That would make life easier, because then I could set up a
separate branch for you to work with. So that, once your feature is
tested and works as expected, we can easily integrate the changes in the
main branch(es). (If all this sounds like gibberish submitting a patch
also works :-).)


Let us know what you think and if we can be of any help!

Looking forward to your contributions!

Lennart Karssen.



On 24/07/12 17:26, Alisa Manning wrote:
> 
> Hello--
> In the past, I've been involved in code contributions to ProbABEL
> (extracting covariance between regression estimates for snp and snp*E
> for interaction tests).
> 
> I've set aside some time this summer to work on implementing a weighted
> Cox regression model in ProbABEL -- the only change that's required in
> the code is to implement robust standard error estimation in the cox
> proportional hazard functionality.
> 
> (Aside: I see that this is a feature request)
> 
> I noticed that the Cox regression model is under active development in
> ProbABEL version 0.2.0.  The purpose of this email is to check in with
> the group regarding my plan:
> 
> 1) check out some latest developers version of the code
> 2) play around with the coxph code (if it isn't fixed)
> 3) evaluate and test in a statistical fashion (I am a biostatistician
> after all!)
> 4) implement robust standard error estimation
> 5) submit patch for review 
> 
> Comments and ideas are welcome.
> 
> Thanks!
> Alisa
> 
> -- 
> 
> Alisa Knodle Manning, Ph.D.
> Postdoctoral Research Fellow
> Broad Institute
> 617-714-7662
> amanning at broadinstitute.org <mailto:amanning at broadinstitute.org>
> 
> 
> 
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 

-- 
-----------------------------------------------
dr. L.C. Karssen
Erasmus MC
Department of Epidemiology
Room Ee-2224

Postbus 2040
3000 CA Rotterdam
The Netherlands

phone: +31-10-7044217
fax: +31-10-7044657
e-mail: l.karssen at erasmusmc.nl
GPG key ID: 0E1D39E3
-----------------------------------------------



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