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

[L.C. Karssen]

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
>>
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