[GenABEL-dev] Roadmap ProbABEL

[Yury Aulchenko]

On Jan 6, 2014, at 23:21, Maarten Kooyman <kooyman at gmail.com> wrote:

> Dear List,
> 
> Lennart and I did discus a roadmap for ProbABEL. We made this roadmap after comparing ProbABEL with other GWAS applications (more on this later). We are welcome for comments, ideas or patches. You will find here a small summary of our discussion.
> 
> 
> -ProbABEL 0.4.3: bugfix release
> - Fix regression in converting numbers from filevector/DatABEL files. Lennart already started on this :http://lists.r-forge.r-project.org/pipermail/genabel-commits/2014-January/000922.html
> 
> -ProbABEL 0.5.0: P-values and Faster
> - Add P-values to output. (Most likely with help of BOOST library)
> - Log likelihood is disabled by default since wald test is better.

In what sense it is better? In principle, it can be argued that the likelihood ratio test is the "better" because of its statistical properties (after all, Wald is an approximation to the LRT); score is "better" because it is faster...

I can imagine that Wald is "better" because of technical reasons (which is totally fine) - but please comment. 

best,
Yurii

> - masking data in matrix before regression in a more effective way. Now this operation is done twice.
> - Vectorize code for palinear with EIGEN library
> - Optimize compiler flags: executables are unnecessary large in size and matrix calculations can go faster.
> - Other fixes/opportunities.
> 
> - ProbABEL 0.5.1: palogist optimisations and bugfixes.
> - Vectorize code for palogist
> - bug fixes
> 
> 
> With kind regards,
> 
> Maarten
> 
> 
> 
> 
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