[GenABEL-dev] Inconsistent headers for ProbABEL outputs (dose vs. probs)

[L.C. Karssen]

Dear Yurii, dear all,

On 12-03-14 09:26, Yury Aulchenko wrote:
> I am for unification + more clear format (name beta_SNP_addA1
> indicates that A1 is effect, and hence A2 is the reference if I
> understand correctly; need to double check as usual) allele (so, format 2)

Glad to hear that you agree.

> 
> "chi2_SNP_A1" is weird though as chi2 does not relate to specific
allele used (would be the same if we swap the reference; it is only Z
whose sign is sensitive to ref/eff alleles)

Good point! I'll need to look into that.

> 
> indeed it may disturb pipelines, so we need to make that very clear etc.


Something for v0.5, not for the upcoming 0.4.3 release.


Thanks for thinking along.

Lennart.

> 
> best wishes,
> Yurii
> 
> On Mar 5, 2014, at 23:10, L.C. Karssen <lennart at karssen.org> wrote:
> 
>> Dear list,
>>
>> For those who haven't followed the discussion on this list I had with
>> Lucho Dimitrov [1], here's a summary:
>>
>> While debugging the problem that ProbABEL's make check gives errors on
>> Solaris we found out that this is due to the use of the -I option to the
>> diff command, which is present in GNU's diff, but not in the Solaris
>> version.
>>
>> The -I option is used to ignore the header line when comparing the
>> output for the additive model calculated with dosage data as input vs.
>> using probability data as input.
>>
>> Lucho wondered why the column headers are different in the first place.
>> A good point, IMHO. The header for dosage-based output is:
>>
>> name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position
>> beta_SNP_add sebeta_SNP_add chi2_SNP
>>
>> For probability-based output, the headers is:
>>
>> name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position
>> beta_SNP_addA1 sebeta_SNP_addA1 chi2_SNP_A1
>>
>> Why don't we harmonise these two headers? I would suggest going with the
>> second header:
>> - it clearly indicates which allele is used as reference when
>> calculating beta
>> - it's consistent with the other probability-base output headers.
>>
>> Pros:
>> - more consistent output
>> - simpler checks
>> - compatibility with other OSes (e.g. Solaris)
>>
>> Cons:
>> - Change of output format may disturb current pipelines (so definitely
>> something for a major increase in version number)
>>
>>
>> What do you think? Any other ideas, pros, cons?
>> For now I've filed a bug for this issue [2]
>>
>> Thanks for thinking along,
>>
>> Lennart.
>>
>>
>> [1]
>> http://lists.r-forge.r-project.org/pipermail/genabel-devel/2014-March/000993.html
>> [2]
>> https://r-forge.r-project.org/tracker/index.php?func=detail&aid=5409&group_id=505&atid=2058
>> -- 
>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>> L.C. Karssen
>> Utrecht
>> The Netherlands
>>
>> lennart at karssen.org
>> http://blog.karssen.org
>> GPG key ID: A88F554A
>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>
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> 

-- 
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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