[Bioc-devel] Valid classes for extraColumnSlots

Fri Aug 29 05:18:26 CEST 2014

Added to S4Vectors. Thanks!

On Thu, Aug 28, 2014 at 5:04 PM, Peter Hickey <hickey at wehi.edu.au> wrote:

> Thanks, Michael. Do you think there's a general use case for a
> replaceROWs, NULL method or shall I just specify that in my package? I
> require it because the slot is matrixOrNULL via a setClassUnion but I don't
> know how common that is amongst other BioC devels.
>
> setMethod("replaceROWS",
>           "NULL",
>           function(x, i, value) {
>             NULL
>           }
> )
>
> Thanks,
> Pete
>
>
> On 29/08/2014, at 8:34 AM, Michael Lawrence <lawrence.michael at gene.com>
> wrote:
>
> > Sorry it took so long. Fixed in S4Vectors 0.1.3. Surprisingly, we were
> missing a replaceROWs,matrix method.
> >
> >
> >
> > On Tue, Aug 26, 2014 at 5:13 PM, Peter Hickey <hickey at wehi.edu.au>
> wrote:
> > Hi Michael,
> >
> > Thanks for your patience. Here is a self-contained example with comments
> https://gist.github.com/PeteHaitch/fdb66d360446ff96ed4b
> >
> > Thanks,
> > Pete
> >
> >
> > On 27/08/2014, at 1:43 AM, Michael Lawrence <lawrence.michael at gene.com>
> wrote:
> >
> > > Do you have the code that actually fails? Then I could use it to
> reproduce the problem and fix things.
> > >
> > > Thanks,
> > > Michael
> > >
> > >
> > > On Tue, Aug 26, 2014 at 4:25 AM, Peter Hickey <hickey at wehi.edu.au>
> wrote:
> > > Hi Michael,
> > >
> > > Sorry for my misunderstanding. Here is some code describing the class
> > >
> https://github.com/PeteHaitch/GenomicTuples/blob/master/R/GTuples-class.R
> > > (the package is not yet installable but hopefully the in-progress code
> > > shows you what I'm trying to achieve).
> > >
> > > The relevant slot is called "internalPos" and extraColumnSlotNames does
> > > indeed return this as a character vector. What I meant is that
> originally
> > > the internalPos slot was a matrix (or NULL). I switched to DataFrame
> > > (or NULL) because I was running into some problems related to
> replaceROWS
> > > when it was a matrix.
> > >
> > > Thanks,
> > > Pete
> > >
> > > ----- Original Message -----
> > > From: Michael Lawrence <lawrence.michael at gene.com>
> > > To: Peter Hickey <hickey at wehi.edu.au>
> > > Cc: bioc-devel at r-project.org
> > > Sent: Tue, 26 Aug 2014 13:35:35 +1000 (EST)
> > > Subject: Re: [Bioc-devel] Valid classes for extraColumnSlots
> > > Hi Peter,
> > > Some code would help here.  I'm not sure what you mean by having a
> matrix as your extraColumnSlots. A derivative of GenomicRanges should
> definel a method for extraColumnSlotNames that returns a character vector
> of names for actual slots that the class defines. It sounds like you're
> trying to represent all of the extra column slots with a single matrix
> slot, which is not how the mechanism was designed.
> > > Michael
> > >
> > > On Mon, Aug 25, 2014 at 7:57 PM, Peter Hickey <hickey at wehi.edu.au>
> wrote:
> > > Are the extraColumnSlots of a class that extends GenomicRanges limited
> to DataFrame objects?
> > >
> > > Background: I wrote a class that extends the GRanges class. It has a
> matrix as the extraColumnSlots. When I use
> replaceROWS,GenomicRanges,GenomicRanges-method (via inheritance) it
> extracts this extraColumnSlots as a DataFrame object by use of
> GenomicRanges:::extraColumnSlotsAsDF. This means that the subsequent call
> to update() in replaceROWS,GenomicRanges,GenomicRanges-method fails because
> the class definition expects a matrix for the extraSlotNames but gets a
> DataFrame.
> > >
> > > In this case, it's not a problem for me to change my extraColumnSlots
> element to a DataFrame in the class definition. However, more generally,
> some guidance on what classes are and are not allowed in extraColumnSlots
> would be appreciated.
> > >
> > > Thanks,
> > > Pete
> > >
> > > This is using BioC devel:
> > > sessionInfo()
> > > R version 3.1.1 (2014-07-10)
> > > Platform: x86_64-apple-darwin13.1.0 (64-bit)
> > >
> > > locale:
> > > [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
> > >
> > > attached base packages:
> > > [1] parallel  stats     graphics  grDevices utils     datasets  methods
> > > [8] base
> > >
> > > other attached packages:
> > > [1] GenomicTuples_0.1.0   GenomicRanges_1.17.35 GenomeInfoDb_1.1.18
> > > [4] IRanges_1.99.24       S4Vectors_0.1.2       BiocGenerics_0.11.4
> > > [7] devtools_1.5
> > >
> > > loaded via a namespace (and not attached):
> > >  [1] Biobase_2.25.0   digest_0.6.4     evaluate_0.5.5   httr_0.4
> > >  [5] memoise_0.2.1    packrat_0.4.0.12 Rcpp_0.11.2      RCurl_1.95-4.3
> > >  [9] stats4_3.1.1     stringr_0.6.2    tools_3.1.1      whisker_0.3-2
> > >
> > > --------------------------------
> > > Peter Hickey,
> > > PhD Student/Research Assistant,
> > > Bioinformatics Division,
> > > Walter and Eliza Hall Institute of Medical Research,
> > > 1G Royal Parade, Parkville, Vic 3052, Australia.
> > > Ph: +613 9345 2324
> > > hickey at wehi.edu.au
> > > http://www.wehi.edu.au
> > >
> > > ______________________________________________________________________
> > > The information in this email is confidential and
> intend...{{dropped:6}}
> > >
> > > _______________________________________________
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> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >
> > > ______________________________________________________________________
> > > The information in this email is confidential and intended solely for
> the addressee.
> > > You must not disclose, forward, print or use it without the permission
> of the sender.
> > > ______________________________________________________________________
> > >
> >
> > --------------------------------
> > Peter Hickey,
> > PhD Student/Research Assistant,
> > Bioinformatics Division,
> > Walter and Eliza Hall Institute of Medical Research,
> > 1G Royal Parade, Parkville, Vic 3052, Australia.
> > Ph: +613 9345 2324
> >
> > hickey at wehi.edu.au
> > http://www.wehi.edu.au
> >
> > ______________________________________________________________________
> > The information in this email is confidential and intended solely for
> the addressee.
> > You must not disclose, forward, print or use it without the permission
> of the sender.
> > ______________________________________________________________________
> >
>
> --------------------------------
> Peter Hickey,
> PhD Student/Research Assistant,
> Bioinformatics Division,
> Walter and Eliza Hall Institute of Medical Research,
> 1G Royal Parade, Parkville, Vic 3052, Australia.
> Ph: +613 9345 2324
>
> hickey at wehi.edu.au
> http://www.wehi.edu.au
>
> ______________________________________________________________________
> The information in this email is confidential and inte...{{dropped:10}}