[GenABEL-dev] export.plink bug: should we change the default?

[L.C. Karssen]

Dear list,

We recently got bitten by bug #2055 (ref [1]) in GenABEL's
export.plink() again. Data was exported to .ped format and everything
seemed to have gone well, however, we later found out that the exported
genotypes were wrong. Exporting to .tped (export.plink(...,
transpose=TRUE)) worked fine.

I think we should change the default for the transpose option to TRUE
and add a warning in case someone sets it to FALSE. I'm of course
willing to write the necessary code.
At least this will safeguard the users from this problem until the
actual bug is fixed.

What are you're thoughts on this?


Best,

Lennart.

[1]
https://r-forge.r-project.org/tracker/index.php?func=detail&aid=2055&group_id=505&atid=2058
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L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

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