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

[Nicola Pirastu]

Dear all,

how about we create a FAQ page on the website or on the forum as sticky topic?


I think we are missing one and this is one of those questions which are bound to come up every once in a while (together with "ProbABEL won't work with 1000G indels imputed with IMPUTE").


Best

Nicola



Il giorno 03/apr/2013, alle ore 13:20, "L.C. Karssen" <lennart at karssen.org> ha scritto:

> 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!
>>>>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>>>>> ------------------------------------------------------------------
>>>>> 
>>>>> _______________________________________________
>>>>> genabel-devel mailing list
>>>>> genabel-devel at lists.r-forge.r-project.org
>>>>> 
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>> 
>>>> --
>>>> -----------------------------------------------------------------
>>>> 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
>>>> ------------------------------------------------------------------
>>>> 
>>>> ,
>>>> _______________________________________________
>>>> genabel-devel mailing list
>>>> genabel-devel at lists.r-forge.r-project.org
>>>> 
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>> _______________________________________________
>>> genabel-devel mailing list
>>> genabel-devel at lists.r-forge.r-project.org
>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>> 
>> 
>> 
>> 
>> 
>> 
>> _______________________________________________
>> genabel-devel mailing list
>> genabel-devel at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> 
> 
> 
> -- 
> -----------------------------------------------------------------
> 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
> ------------------------------------------------------------------
> 
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel