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.mich...@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 <hic...@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.mich...@gene.com> > To: Peter Hickey <hic...@wehi.edu.au> > Cc: bioc-devel@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 <hic...@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 > hic...@wehi.edu.au > http://www.wehi.edu.au > > ______________________________________________________________________ > The information in this email is confidential and intend...{{dropped:6}} > > _______________________________________________ > Bioc-devel@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 hic...@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. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
