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

[L.C. Karssen]

Hi Yurii, Maria,

Indeed, this is more a workaround than a fix. I think we communicated
this simple workaround in the past, but I agree with Maria we should
either announce it more widely, or, probably better push a new GenABEL
release to CRAN (for those people who don't read the announcements :-)).

Yurii, what do you think? One the one hand it is not urgent (we've been
living with this bug for a while) on the other hand, the present
situation is a dangerous one... Are there any developments in GenABEL
SVN that are not ready for publishing yet?


Best,

Lennart.

On 04/03/2013 12:19 PM, Yurii Aulchenko wrote:
> Hi Maria,
> 
> if my understanding is correct, the fix is now only in the devel-version on
> SVN - so you would need to export and build package if you really want it
> (see http://genabel.r-forge.r-project.org/tutHowToInstallDevelVersion.html).
> 
> But the 'fix' is very simple (and is not actually fixing anything - just
> trying to avoid confusion!): the default option now is set to
> 'transpose=TRUE'. So you can simply set this up manually when calling
> 'export.plink' :)
> 
> Yurii
> 
> 
> On Wed, Apr 3, 2013 at 11:58 AM, Maria G <mgmaria at yandex.ru> wrote:
> 
>> 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
>>>>
>>>>  Stuur mij aub geen Word of Powerpoint bestanden!
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>>>>  ------------------------------------------------------------------
>>>>
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>>>>
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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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> 
> 
> 
> 
> 
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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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