[Bioc-devel] Fwd: proteomics/MS generic

Laurent Gatto lg390 at cam.ac.uk
Sat Feb 28 16:24:51 CET 2015


Dear proteomics developers,

There is now a new ProtGenerics package that defines generic functions
that are used in different MS/proteomics packages. Currently, it defines

  ## previously defined in mzR
  setGeneric("psms", function(object, ...) standardGeneric("psms"))
  setGeneric("peaks", function(object, ...) standardGeneric("peaks")) 
  setGeneric("modifications", function(object, ...) standardGeneric("modifications"))
  setGeneric("database", function(object, ...) standardGeneric("database"))
  
  ## previously defined in MSnbase
  setGeneric("rtime", function(object, ...) standardGeneric("rtime")) 
  setGeneric("tic", function(object, ...) standardGeneric("tic"))
  setGeneric("spectra", function(object, ...) standardGeneric("spectra"))
  setGeneric("intensity", function(object, ...) standardGeneric("intensity"))
  setGeneric("mz", function(object, ...) standardGeneric("mz"))
  
  ## new 
  setGeneric("peptides", function(object, ...) standardGeneric("peptides"))
  setGeneric("proteins", function(object, ...) standardGeneric("proteins"))
  setGeneric("accessions", function(object, ...) standardGeneric("accessions"))
  setGeneric("scans", function(object, ...) standardGeneric("scans"))
  setGeneric("mass", function(object, ...) standardGeneric("mass"))
  setGeneric("ions", function(object, ...) standardGeneric("ions"))
  setGeneric("chromatograms", function(object, ...) standardGeneric("chromatograms")) 

If there is a need for additional generic functions in ProtGenerics,
please send a PR on the github page or open an issue. If any of the
generics above have a scope outside of proteomics, they will be moved to
BiocGenerics.

Best wishes,

Laurent

On 14 January 2015 19:03, Laurent Gatto wrote:

> Dear Bioconductor team,
>
> Following up from an email from last November, here is a list of
> generics that could be added to BiocGenerics to avoid conflict and
> unnecessary dependencies among proteomics packages:
>
> ## currently in mzR
> setGeneric("psms", function(object, ...) standardGeneric("psms"))
> setGeneric("peaks", function(object, ...) standardGeneric("peaks")) 
> setGeneric("modifications", function(object, ...) standardGeneric("modifications"))
> setGeneric("database", function(object, ...) standardGeneric("database"))
>
> ## currently in MSnbase
> setGeneric("rtime", function(object, ...) standardGeneric("rtime")) 
> setGeneric("tic", function(object, ...) standardGeneric("tic"))
> setGeneric("spectra", function(object, ...) standardGeneric("spectra"))
> setGeneric("intensity", function(object, ...) standardGeneric("intensity"))
> setGeneric("mz", function(object, ...) standardGeneric("mz"))
>
> ## new 
> setGeneric("peptides", function(object, ...) standardGeneric("peptides"))
> setGeneric("proteins", function(object, ...) standardGeneric("proteins"))
> setGeneric("accessions", function(object, ...) standardGeneric("accessions"))
> setGeneric("scans", function(object, ...) standardGeneric("scans"))
> setGeneric("mass", function(object, ...) standardGeneric("mass"))
> setGeneric("ions", function(object, ...) standardGeneric("ions"))
> setGeneric("chromatograms", function(object, ...) standardGeneric("chromatograms")) 
> ## rather than chroms, as suggested by Thomas, which could also match chromosomes
>
> I am happy to submit a patch against BiocGenerics, if useful.
>
> I think that links and groups are very general for an inclusion on the
> grounds of proteomics/mass spec needs. I will leave if to the
> BiocGenerics maintainers.
>
>
> On a related note, could the score generic be moved from IRanges to
> BiocGeneric? It also exists in mzR, albeit with different signature:
>
> IRanges: 
>
>  setGeneric("score", function(x, ...) standardGeneric("score"))
>
> mzR:
>
>  setGeneric("score", function(object) standardGeneric("score"))
>
>
> Similarly, fileName is defined in annotate
>
>    if (is.null(getGeneric("fileName")))
>         setGeneric("fileName", function(object, ...)
>                    standardGeneric("fileName"))
>                    
> and mzR
>
>   setGeneric("fileName", function(object) standardGeneric("fileName"))
>
> I will make sure that the packages I maintain will comply with any of
> the above changes.
>
>
> Best wishes,
>
> Laurent
>
> On 18 November 2014 12:55, Laurent Gatto wrote:
>
>> Dear all,
>>
>> We are staring to defined generics repeatedly in MS and proteomics
>> packages (mzR, mzID, MSnID, MSnbase, ...) and thought that these could
>> be candidates for BiocGenerics. A few suggestions are
>>
>> setGeneric("psms", function(object, ...) standardGeneric("psms"))
>> setGeneric("peaks", function(object, scans,...) standardGeneric("peaks"))
>> setGenerix("modifications", function(object, ...) standardGeneric("modifications"))
>> setGeneric("database", function(object, ...) standardGeneric("database"))
>> setGeneric("peptides", function(object, ...) standardGeneric("peptides"))
>>
>> And maybe
>>
>> setGeneric("spectra", function(object, ...) standardGeneric("spectra"))
>> setGeneric("scans", function(object, ...) standardGeneric("scans"))
>>
>> Other suggestions from Vlad and Thomas include
>>
>> - proteins, accessions
>> - ions, chroms, links and groups
>>
>> Please share other suggestions and comments.
>>
>> If we come up with a list of useful candidates and the BiocGenerics
>> maintainers see this as a useful contribution, I am happy to send a
>> patch with relevant generic definitions and Rd files.
>>
>> Best wishes,
>>
>> Laurent

-- 
Laurent Gatto
http://cpu.sysbiol.cam.ac.uk/



More information about the Bioc-devel mailing list