[Bioc-devel] Valid classes for extraColumnSlots

[Michael Lawrence]

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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