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