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

[Yurii Aulchenko]

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

boost: no experience

So I would personally be more inclined towards GSL, but only because I had
some experience with it. 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?

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.

Yurii

PS what is p.o.p. code?

On Fri, May 24, 2013 at 2:55 AM, L.C. Karssen <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
> http://blog.karssen.org
>
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
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