fix for issue #755 (chromatogram() call with msLevel = 2L); improve documentation (and vignette) for this.
change the estimatePrecursorIntensity() function to a method and import the generic from ProtGenerics. This ensures we can have different implementations for XcmsExperiment, XCMSnExp and also avoid clashes with the implementation in Spectra for Spectra objects.
add a function that allows coercion of a XcmsExperiment to XCMSnExp for backward compatibility.
This PR adds:
chromatogram()call withmsLevel = 2L); improve documentation (and vignette) for this.estimatePrecursorIntensity()function to a method and import the generic from ProtGenerics. This ensures we can have different implementations forXcmsExperiment,XCMSnExpand also avoid clashes with the implementation in Spectra forSpectraobjects.XcmsExperimenttoXCMSnExpfor backward compatibility.