[Bioc-devel] Fwd: proteomics/MS generic

[Laurent Gatto]

On 28 February 2015 15:24, Laurent Gatto wrote:

> 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. 

URL: https://github.com/lgatto/ProtGenerics

> 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