[Bioc-devel] Fwd: proteomics/MS generic

Laurent Gatto lg390 at cam.ac.uk
Tue Nov 18 12:55:12 CET 2014

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 Gatto

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