[Bioc-devel] Valid classes for extraColumnSlots

[Peter Hickey]

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
> >
> > ______________________________________________________________________
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> >
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> >
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> >
> 
> --------------------------------
> 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:25}}