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

Wed Apr 3 13:33:13 CEST 2013

I am - in general - for it. Something like 'current bugs and workarounds'?
We will need to keep this updated (e.g. when problem gets eventually fixed,
update the entry).

Yurii

On Wed, Apr 3, 2013 at 1:25 PM, Nicola Pirastu <pirastu at burlo.trieste.it>wrote:

> 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
>
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