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

[Yurii Aulchenko]

Agree: seems to be the best option in sake of time

On Thu, Oct 4, 2012 at 1:06 AM, L.C. Karssen <lennart at karssen.org> wrote:

> Dear all,
>
> In order to close this bug I've decided to go with option (1): fix the
> documentation. This fix is committed in SVN r.971.
>
>
> Best,
>
> Lennart.
>
>
>
> On 16-07-12 15:44, L.C. Karssen wrote:
> > On 07/14/2012 04:13 PM, Yurii Aulchenko wrote:
> >> 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.
> >
> > At the moment the test is:
> >
> >       if (fabs(mli.Rsq[csnp])<1.e-16) poly=0;
> >
> > Isn't that threshold of 1e-16 too low? I observe in our imputations
> > using the 1kG phase 1 alpha reference that only for monomorphic SNPs we
> > get an Rsq of 0.0, the lowest Rsq for a non-monomorphic SNP is 1e-5.
> > Wouldn't a cut-off of 0.3 (as is regularly done in meta-analysis) be
> > better? Or, to give some room, use 0.1?
> >
> > Anyway, don't you think we should print a warning message to stderr that
> > says something like: "Warning: one or more of your SNPs have a very low
> > imputation quality (Rsq < 0.1) and consequently their effect estimates
> > are set to 'nan'"?
> >
> >
> > Thanks,
> >
> > Lennart.
> >
> >
> >>
> >> 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
> >>> 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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> >>>
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> >>
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> >>
> >
> >
> >
> >
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> >
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> >
>
> --
> -----------------------------------------------------------------
> 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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