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

[Maria G]

Dear Lennart,

that's really helpful, thank you! 

Does it mean I have to update the version of GenABEL to get read of the bug? Which version is fine?


best
Mariya

02.04.2013, 20:30, "L.C. Karssen" <lennart at karssen.org>:
> 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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