[Bioc-devel] Fwd: proteomics/MS generic

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