[GenABEL-dev] Bug #1247; ProbABEL: what to do with Rsq in info file

[Yurii Aulchenko]

I would go for (1) - when Rsq is indeed zero or very close to zero,
nonsense results are obtained. Generates a lot of confusion, and this
is why the check is there.

Yurii

----------------------
Yurii Aulchenko
(sent from mobile device)

On 13 Jul 2012, at 19:46, "L.C. Karssen" <lennart at karssen.org> wrote:

> Dear list,
>
> As pointed out on the forum
> (http://forum.genabel.org/viewtopic.php?f=10&t=663&p=1145#p1145) the
> ProbABEL manual states that the contents of the info file is not
> relevant for the ProbABEL output and is simply copied over.
>
> It turns out that this is not the case (see also bug #2147:
> https://r-forge.r-project.org/tracker/index.php?func=detail&aid=2147&group_id=505&atid=2058).
>
> In main.cpp line 751 we test for the Rsq values taken from the info
> file. The test is used to decide whether to output betas, se_betas etc.
> as 'nan' in the output files (see lines 771 and 836 in main.cpp).
>
> I see two possible solutions:
> 1) update the manual and say that the Rsq column in the info file should
> contain non-zero values. How many people will be using ProbABEL with
> 'fake' info files?
>
> 2) remove of modify the Rsq test in main.cpp. Suggestions are welcome on
> a sane way to implement this. Print a warning message?
>
>
> Thanks for thinking along,
>
> Lennart.
> --
> -----------------------------------------------------------------
> L.C. Karssen
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>
> lennart at karssen.org
> http://blog.karssen.org
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