Add a bpc,MSnExp and bpc,OnDiskMSnExp method

[jorainer]

Would be nice to have, along with the tic method, also a bpc method that extracts the base peak chromatogram from an MSnExp and OnDiskMSnExp, i.e. the maximum intensity from each spectrum.

If you would agree I could implement that.

[lgatto]

Do you mean a method that extract the basePeakIntensity feature data? Note that this data isn't available from (in memory) MSnExp objects (i.e. in the Spectrum1/Spectrum2 objects). It would need to be calculated on the fly, and I wouldn't be surprised if they didn't match fData values, or would not be after some processing. We already had this discussion, I think, of such data that would not be correct after some processing, and agreed to rename it as original or initial.

Or go you mean something like chromatogram?

But yes, it would be useful to have such a method.

[jorainer]

I guess yes, extract the basePeakIntensity feature data - haven't looked at that yet. That might however be like the totIonCurrent feature data, that represents the raw data from the MS-machine and does not match - at least for our files - the value of the centroided mzML file.

I didn't check the chromatogram method yet, eventually that does what I want. In the end would be nice to have some method to extract sum or max of intensities of a spectrum.
Actually, thinking it over an implementation of the chromatogram method might be it, with a parameter type that can be either "tic" or "bpc" and eventually a logical parameter initial to specify whether the values should be extracted from the feature data.

[lgatto]

I guess yes, extract the basePeakIntensity feature data - haven't looked at that yet. That might however be like the totIonCurrent feature data, that represents the raw data from the MS-machine and does not match - at least for our files - the value of the centroided mzML file.

Yes, same situation - I'm fine with having a bpi,OnDiskMSnExp method that returns that feature data, and document that these are the values are reported in the raw data. Not sure if we need bpi,MSnExp, that iterates over all spectra. If so, then we could have a parameter in bpi,OnDiskMSnExp that forces to recalculate the values. What do you think?

I didn't check the chromatogram method yet

There's also xic, for extracted ion chromatograms.

chromatogram and xic would be very easy to implement for OnDiskMSnExp, as they operate on an mzRramp object, that we can create (and close) from fileNames(.).

In the end would be nice to have some method to extract sum or max of intensities of a spectrum.

Could you clarify what you mean? The max or sum of all intensities in a spectrum? That would be easy to add - something along the lines of

• quantify(sp, method = "max") would return max(intensity(sp))
• quantify(sp, method = "sum") would return sum(intensity(sp))

(There's already a method = "sum" withreporters` defined)

[jorainer]

Done. The bpi method has an additional parameter initial that, when TRUE returns the values extracted from the mzML header and when FALSE calculates it from the actual data. I have modified the tic,OnDiskMSnExp method the same way (i.e. parameter initial) and modified the documentation accordingly.