[GenABEL-dev] mmscore_regression() in ProbABEL: code review

[Maarten Kooyman]

Hi Lennart,

This seems alright to me. The most time consuming step is multiplication 
of the variance-covariance matrix, which I optimised. Since this is the 
same, I do not expect any big change in performance. With every commit 
done for ProbABEL my personal Jenkins instance benchmark 3 scenario's:

Palinear with DatABEL  files 
((Npeople=3485,Npredictor=1,Nsnp=33815,correct for sex and age)
Palinear with mldose files (Npeople=3485,Npredictor=1,Nsnp=33815,correct 
for sex and age)
Palinear with DatABEL files and mmscore( 
Npeople=500,Npredictor=1,Nsnp=1000).

When there is a slow down (or speed up!) I will inform you.

Kind regards,

Maarten


On 09-05-14 17:03, L.C. Karssen wrote:
> Dear list (and Maarten in particular),
>
> I've written some Doxygen documentation for the mmscore_regression()
> function that Maarten recently created. While doing so I changed some of
> the variable names to be a bit more understandable and documented what
> the function does according to Diego's suggestion on this list some time
> ago. I also slightly changed the variables that are created in the
> function to get rid of one transpose() action.
>
> My question is: could you have a look at the code (lines 57--62) in the
> attached file and see if this still preservers the vectorisation
> potential as mentioned in Maarten's comment in the code?
>
> The function can be found in reg1.cpp.
>
>
> Thanks a lot,
>
> Lennart.
>
>
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