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

[L.C. Karssen]

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.
-- 
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L.C. Karssen
Utrecht
The Netherlands

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

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