The coming MSsary package is going to use scans, ions, chroms, peaks,
links, and groups heavily for accessing underlying MS data - if any of
these, apart for those already mentioned, are used by others they would be
candidates?
With regards to the peaks generic currently defined in mzR, do you have
specific dispatch on the scans argument since it is in the generic?
Otherwise I would argue that it should be removed once it is migrated to
Biogenerics? (another thing I?ve never understood is why you have opted for
?peaks?, instead of ?scans? or ?spectra? as this is essentially what it
returns, but that is another discussion : )
best
Thomas
On 18 Nov 2014, at 00:01, Vladislav Petyuk <petyuk at gmail.com> wrote:
A couple more
* proteins
* accessions
I use accessions as a broader term of protein sequence ID (e.g. in
stop-to-stop six frame translation).
On Mon, Nov 17, 2014 at 2:49 PM, Laurent Gatto <lg390 at cam.ac.uk> 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"))
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