[Bioc-devel] proteomics/MS generic

[Vladislav Petyuk]

I concur on "peaks" vs "scans" or "spectra" issues.  One have to run peak
picking algorithm to get peaks out of a spectrum.  Therefore I'd vote for
"spectra".

On Tue, Nov 18, 2014 at 12:23 AM, Thomas Lin Pedersen <thomasp85 at gmail.com>
wrote:

> 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
>>
>
>
>

	[[alternative HTML version deleted]]