[GenABEL-dev] Interesting idea by Gulnara Svischeva

[L.C. Karssen]

Dear list,

I was going through the changelog of GenABEL and saw that Gulya's
poly_eigen is the default method for polygenic() since version 1.6-8. I
did a quick comparison on the computation speed of the three methods
(polygenic_hglm, polygenic with polylik and with poly_eigen) on our
population and even though I knew what to expect from Yurii's results, I
am still impressed at the speedup! 

I was wondering, is there a publication on this method/implementation?
Has there been any comparison of poly_eigen vs. the old method (in terms
of variance, lambda etc.? In February/March this year there was a
discussion on this list where Yurii compared the polylik method with
polygenic_hglm, but I haven't seen anything similar on the poly_eigen
method.


Enjoy the weekend,

Lennart.


On vr, 2011-05-20 at 21:16 +0200, Yurii Aulchenko wrote:
> In attached PDF I show the timing for running 'polygenic' (red line;
> ML operating on Gulya's idea), polygenic_hglm (black; Xia/Lars), and
> REML.rotate (green; Lars's implementation/extension of Gulya's idea)
> as a function of sample size (X axes).
> 
> While polygenic and hglm show exponential trend, REMLrotate line is
> not only the lowest, but also looks almost linear to me (also looking
> at the code, it should be roughly linear on time with no of subjects).
> So, with REMLrotate we can get arbitrary big speed-up (x100, x1000,
> x10000, ... you name it!) cf other methods, just by adding more people
> to the data :) Not a bad result!
> 
> Lars and Gulya, you are the champions!
> 
> best wishes,
> Yurii
> 
> 2011/5/19 Yurii Aulchenko <yurii.aulchenko at gmail.com>:
> > Correction: as Lars spotted out, I did placed my 'tags' wrongly
> > concerning time performance results, so actually REML.rotate is the
> > fastest.
> >
> > Here are updated results:
> >
> >> With conv=1e-8 mean time for estimation on 300 IDs was:
> >>
> > 17.81 sec for polygenic_hglm
> >> 2.27 sec for 'polygenic'-ML
> > 1.33 sec for REML.rotate
> >
> > best wishes, and sorry for inconvenience,
> > Yurii
> >
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-- 
-----------------------------------------------
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
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