[Bioc-devel] Valid classes for extraColumnSlots

[Michael Lawrence]

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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