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

[Yurii Aulchenko]

In theory I agree :)

In practice submitting to CRAN takes from 4 hours to a full day, so I
personally would not like to submit unless strictly necessary.

As for this particular fix - I expect some more code changes still this
week, so if we decide to publish on CRAN I would wait till next week.

best wishes,
YA

On Wed, Apr 3, 2013 at 1:20 PM, L.C. Karssen <lennart at karssen.org> wrote:

> 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
> >>> ------------------------------------------------------------------
> >>>
> >>> ,
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> >>>
> >>
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> >>
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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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