[GenABEL-dev] Partial fix of ProbABEL Cox module

[L.C. Karssen]

Dear list,

Over the past few weeks I've been working on fixing ProbABEL's Cox PH
module. This has been very high on our wish list.

First a short piece of history: after the integration of the filevector
library around ProbABEL v0.1-9 the Cox module stopped working. We have
since fixed a few bugs in the older v0.1-3 release (with sponsorship
from prof. Kiemeney at the Radboud Medical Centre in Nijmegen). At the
time we estimated that finding the problem in the new(er) code base
would take too much time.

Thanks to Maarten Kooyman's work on code refactoring and the integration
of the Eigen matrix library I have been able to (so partially) fix
pacoxph, see commit r.1080 in SVN. (I had been working on this using
ProbABEL trunk, but waited with committing to SVN until v0.3.0 was
released, to keep things clear.)

At the moment the code works when dose files are used as input (either
in plain text format or in filevector format). This I verified with the
R checks in the v.0.1-3 pacox-fix branch.
Also, when using probability data as input there is no difference in the
output when using text and fv files as input. Unfortunately there still
is a difference in the dose vs. prob as input.

I have been able to fix the dose vs. prob problem as well, but that
meant commenting the section of "if(is_interaction_excluded)" in
src/reg1.cpp lines 175--200. I see two possibilities here:
1) Something is wrong with the is_interaction_excluded option in general
2) Something went wrong in the code refactoring

In order to find out which of these two options is the culprit it would
help enormously (saving a lot of time) if someone could explain me the
use of this parameter. Has this part of the code actually been tested?
We don't seem to have examples/tests for this part of the code.


Thanks for looking into this!
Best,

Lennart.

-- 
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L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

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