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[Bioc-devel] adding methods to BiocGenerics

6 messages · Laurent Gatto, Martin Morgan, Michael Lawrence +1 more

Original
Stephanie M. Gogarten
# 
Dear Core Team,

What do you think about adding the following generics to BiocGenerics?

colData
rowRanges
ref
alt
qual
filt
header
fixed
info
geno

They are currently defined by both 
VariantAnnotation/SummarizedExperiment and SeqArray. Given the 
increasingly widespread use of VCF files, it seems likely that other 
packages may want to use them in future also.

Stephanie
Laurent Gatto
#
On 19 May 2017 15:39, Stephanie M. Gogarten wrote:

            

      
      
      
    

        
Currently exists in MSnbase with signature

  setGeneric("qual", function(object) standardGeneric("qual"))

As far as I know, only used in that packages. I'm more than happy to use
BiocGenerics::qual when/if it becomes available.

            

      
      
      
    

        
Currently exists in mzR with signature

  setGeneric("header", function(object, scans, ...) standardGeneric("header"))

and is used at least in mzR and MSnbase.

I guess that signature, as it is, wouldn't be a good for BiocGenerics.

Best wishes,

Laurent

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Michael Lawrence
    

    

      
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Since SeqArray already imports SummarizedExperiment and
VariantAnnotation, why can't it just move them to Depends and use
their generics?

On Fri, May 19, 2017 at 8:39 AM, Stephanie M. Gogarten

        
<sdmorris at u.washington.edu> wrote:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Martin Morgan
    

    

      
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On 05/19/2017 12:14 PM, Michael Lawrence wrote:

            

      
      
      
    

        
do they need to be moved to Depends? Or simply import the generic export 
the new method(s) (and generic)?

Martin

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        
This email message may contain legally privileged and/or...{{dropped:2}}

  
  


  


      

    

    

      
      

        


  

        

      Michael Lawrence
    

    

      
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That could work, also.

On Fri, May 19, 2017 at 10:27 AM, Martin Morgan

        
<martin.morgan at roswellpark.org> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Stephanie M. Gogarten
    

    

      
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On 5/19/17 12:15 PM, Michael Lawrence wrote:

            

      
      
      
    

        
We used to do this, but Xiuwen just moved SummarizedExperiment and 
VariantAnnotation from Imports to Suggests, because it was taking too 
long to load the package with them attached. So now we are redefining 
the generics.

In our daily use of SeqArray we almost never use VariantAnnotation or 
these generics, so the change improves our pipeline performance without 
any immediate downsides for us. But it does add annoyance for any 
(potential) users of both SeqArray and VariantAnnotation in the same 
session, as they would have to add the package name with "::" to 
disambiguate the methods.