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

[L.C. Karssen]

Thanks Maarten!
I just committed my changes. Let me know if this changes the benchmark
(for better or worse).


Best,

Lennart.

On 11-05-14 11:49, Maarten Kooyman wrote:
> 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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> 
> 
> 
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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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