[Bioc-devel] Fwd: proteomics/MS generic

[Laurent Gatto]

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/