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

[Yury Aulchenko]

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)

"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)

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

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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