Coerce Spectra to MSnExp

lgatto / MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics

http://lgatto.github.io/MSnbase/

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Coerce Spectra to MSnExp #526

Closed lgatto closed 3 years ago

lgatto commented 3 years ago

This seem not to be possible with the new Spectra from the Spectra package.

> as(spectras, "MSnExp")

Fejl i as(spectras, "MSnExp") : 
  no method or default for coercing "Spectra" to "MSnExp"

Originally posted by @stanstrup in https://github.com/lgatto/MSnbase/issues/508#issuecomment-701261318

lgatto commented 3 years ago

I think I understand what is happening here. The Spectra mentioned in that post isn't the class defined in the new Spectra package, but a first iteration thereof in the MSnbase package (that eventually triggered the development of new packages and the R for Mass Spectrometry initiative.

That class in MSnbase has been renamed MSpectra (see this commit). Sorry for the confusion.

lgatto commented 3 years ago

Closing now, but @stanstrup feel free to follow up.

stanstrup commented 3 years ago

Isn't it still relevant? Or should there be another route to be able to make an mgf from a Spectra object?

lgatto commented 3 years ago

If you mean Spectra::Spectra, there's the export() method.
If you mean MSnbase::MSpectra, then the previous code should work by using the new MSpectra name. If not, then feel free to follow up, as this would need to be investigated.

Another question is whether we want to be able to coerce MSnbase::MSnExp to Spectra::Spectra. Possible, but probably not a priority.

stanstrup commented 3 years ago

Ah, yes, right. Then we are back to whether or not that is currently working as intended https://github.com/rformassspectrometry/MsBackendMgf/issues/4

lgatto commented 3 years ago

ok, thanks.