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

[Maria G]

Dear Lennart,

I've tried both on a small data-set:
export.plink(transpose=FALSE) and export.plink(transpose=TRUE) , 
and the output genotypes look both correct... 
Can it be that the bug is not always "active"?

best
Mascha

28.03.2013, 17:34, "L.C. Karssen" <lennart at karssen.org>:
> 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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>
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