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

[L.C. Karssen]

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
-- 
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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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