[GenABEL-dev] Implementing p-value output in ProbABEL

[L.C. Karssen]

Hi Yurii,

Thanks for your insights!

On 26-05-13 09:22, Yurii Aulchenko wrote:
> R: that may be too much to ask to install R as a 'library' :) however,
> similarly to boost, this may provide with more opportunities in the future
> 
> GSL: to my experience should work across major platforms (at least I
> remember compiling MixABEL for Win, and I am using MixABEL for Mac);
> using GSL in MixABEL worked rather straightforwardly

Good to hear that. I do find GSL's matrix/vector code a hassle to use.
> 
> boost: no experience
> 
> So I would personally be more inclined towards GSL, but only because I
> had some experience with it.

In fact, of all options I presented I also only have actual experience
(beyond a few simple tests) with the GSL.

> I have however heard that GSL is
> not-so-perfect library ... so it may appear that eventually you want to
> switch to boost - but for one function that should not be a big deal, right?

Probably not. Can you say something more about GSL being not so perfect?

> 
> Thinking of the future, boost may indeed be the best option, but I
> would definitely do some testing on different platforms. If you give me
> clear instructions, I am willing to do testing for Mac. 

Great!


> 
> Yurii
> 
> PS what is p.o.p. code?

Proof of principle.


Best,

Lennart.

> 
> On Fri, May 24, 2013 at 2:55 AM, L.C. Karssen <lennart at karssen.org
> <mailto:lennart at karssen.org>> wrote:
> 
>     Dear list,
> 
>     One of the long standing feature requests for ProbABEL (#2086 in the
>     tracker) has been adding p-values to the output files (at least for the
>     most-often used additive model based on dosage files).
>     Maarten and I have discussed this a while ago and we'd like to implement
>     this (Maarten actually already wrote a proof of principle).
> 
>     Before we go for a certain implementation I'd like to start a discussion
>     on this list on how to deal with dependencies.
>     For this specific example we have the following options:
>     1) Implement p-value code ourselves (from scratch)
>     2) Use the R math library
>     3) Use the GNU Scientific Library
>     4) Use the Boost library
> 
>     Option 1 is a bad one, because writing good code for extreme p-values is
>     not trivial and this problem has already been solved (by at least the
>     three other options in the list).
> 
>     As to options 2-4 I'd like to hear your opinion on the following:
>     a) introducing dependencies on external libraries: with any of these
>     solutions we introduce a dependency for the people running ProbABEL.
>     Option 2 depends on R being present, 3 on the installation of the GSL
>     and option 3 on Boost. Note that (for efficient matrix math we already
>     recommend installing the Eigen headers, but that is only necessary when
>     compiling, not when running).
>     Personally I don't see this as a bad thing, especially since I can use
>     the ./configure mechanism to disable the feature if the lib is not
>     installed
>     b) which lib would be best to use? Option 2 is easy (and we have
>     Maarten's p.o.p. code based on that). Option 3 would have been my first
>     choice and is also not difficult to program (also the GSL has been shown
>     to have a stable implementation for low p-values [1]). Option 3 is more
>     complex to program, but given the wide range of the Boost libs, we may
>     be able to leverage some of its other features as well (e.g.
>     reading/writing gzipped files).
> 
>     So in short:
>     ad 2) easy, but large dependency on R (will probably also work on
>     Windows)
>     ad 3) easy, simple, but may be more difficult for Windows (needs to be
>     checked)
>     ad 4) more difficult, but more possibilities for the future
> 
> 
>     Any thoughts/suggestions?
> 
>     Thanks,
> 
>     Lennart.
>     --
>     -----------------------------------------------------------------
>     L.C. Karssen
>     Utrecht
>     The Netherlands
> 
>     lennart at karssen.org <mailto:lennart at karssen.org>
>     http://blog.karssen.org
> 
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> 
> 
> -- 
> -----------------------------------------------------
> Yurii S. Aulchenko
> 
> [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
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> <http://yurii-aulchenko.blogspot.nl/> ]

-- 
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L.C. Karssen
Utrecht
The Netherlands

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

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