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

[L.C. Karssen]

Dear list,

As I didn't get any comments to dissuade me, I've just committed a
change that sets the default behaviour of export.plink() in GenABEL to
export .tped/.tfam files. This works around bug #2055.


Best,

Lennart.

On 28/03/13 14:34, L.C. Karssen wrote:
> 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
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
> 
> lennart at karssen.org
> http://blog.karssen.org
> 
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L.C. Karssen
Utrecht
The Netherlands

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

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
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