Extracting MS level > 1 chromatogram

[jorainer]

chromatogram,MSnExp does not allow to extract Chromatograms for MS level > 1 yet. I didn't anticipate that this will be needed, but with SWATH data it is (see sneumann/xcms#205).
The required code is ready in .extractMultipleChromatograms but I didn't add the msLevel argument to chromatograms,MSnExp (yet).
@lgatto: OK if I add that and push to master?

[lgatto]

Yes, of course. Will msLevel be limited to a single level (a numeric of length 1) or will it support multiple levels?

[jorainer]

good point - as of now it supports length > 1. But I'm not sure whether that's clever. Never done anything with MS level > 1. What do you think? restrict to single level?

[lgatto]

I can't think of a use case with more than on level, but I don't think that's a reason to restrict it to one level. Maybe it's good to support it, as long as it's easy to get the levels back from an Chromatograms object.

[jorainer]

OK, so I'll have to add a slot msLevel to the Chromatogram class. That will then be an integer of length > 0.