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 inte...{{dropped:10}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
