[Bioc-devel] Valid classes for extraColumnSlots

Added to S4Vectors. Thanks!


On Thu, Aug 28, 2014 at 5:04 PM, Peter Hickey <hickey at wehi.edu.au> wrote:
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

--------------------------------
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

--------------------------------
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