[Bioc-devel] Valid classes for extraColumnSlots

[Peter Hickey]

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
> 
> ______________________________________________________________________
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--------------------------------
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

______________________________________________________________________
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