[Bioc-devel] Valid classes for extraColumnSlots
Dan Tenenbaum
dtenenba at fhcrc.org
Wed Sep 3 07:57:10 CEST 2014
----- Original Message -----
> From: "Peter Hickey" <hickey at wehi.EDU.AU>
> To: "Michael Lawrence" <lawrence.michael at gene.com>
> Cc: bioc-devel at r-project.org
> Sent: Tuesday, September 2, 2014 7:24:12 PM
> Subject: Re: [Bioc-devel] Valid classes for extraColumnSlots
>
> Hi Michael,
>
> Sorry to bring this up again. I think the S4Vectors version number
> needs to be bumped to propagate the addition of
> replaceROWS,NULL-method to the build system - I can use it if I
> build S4Vectors from source but not if I install via biocLite()
> [with useDevel()].
I've bumped the version (to 0.1.4); this should be available via biocLite() sometime Thursday morning (Seattle time).
Dan
>
> Thanks,
> Pete
>
>
> On 29/08/2014, at 1:18 PM, Michael Lawrence
> <lawrence.michael at gene.com> wrote:
>
> > 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}}
> > > >
> > > > _______________________________________________
> > > > Bioc-devel at r-project.org mailing list
> > > > 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:28}}
>
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