Add peaksVariables function

jorainer commented 2 years ago

This PR:

adds the peaksVariables,MsBackend method to list the available peaks variables from a backend. The default is "mz" and "intensity", but backends such as the MsBackendTimsTof would also have ion mobility or other peak-related information available.
change peaksData,MsBackend to include a new parameter columns = peaksVariables().

Open for discussion:

how should we handle the existing peaksData implementations? So far I have only added ... and hence the columns parameter would be ignored for the MsBackendMzR, MsBackendDataFrame et al backends.
should we change peaksData,Spectra to include a parameter columns = peaksData(object) or should we support passing that parameter using ...?

jorainer commented 2 years ago

Any opinion on that @lgatto or @sgibb ?

sgibb commented 2 years ago

I am in favour for a column argument in peaksData,Spectra. So it is very obvious what you get (a matrix with column columns).

jorainer commented 2 years ago

I'll work on that and convert to a PR again once I'm done.

jorainer commented 2 years ago

Some general info:

peaksData,Spectra gained parameter columns which is passed down to peaksData,MsBackend.
The backends in Spectra support only columns "mz" and "intensity", but in any arbitrary order.
This PR will most likely break existing backends because they don't yet support the paramter columns - but I will fix these later.

jorainer commented 2 years ago

OK for review @sgibb and @lgatto :)

rformassspectrometry / Spectra