[Bioc-devel] Valid classes for extraColumnSlots
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 inte...{{dropped:25}}