XCMS3: review fillChromPeaks/fillpeaks parameters about tools-metabolomics

[jorainer]

they will be advanced parameters. some people might want to have them (because they help avoiding that even after filling in missing peaks you still have missing values) but most will not.

[jorainer]

You don't need the method parameter anymore. The XCMSnExp object keeps track of what has been performed. It contains also the parameter object that was used for the chromatographic peak detection. Depending on that it uses the correct approach to fill in missing peak data. For MatchedFilterParam it fills in data from the profile matrix while it uses the raw data for others (like CentWaveParam). Previously, peak data was always integrated from the profile matrix, even if peak detection was, e.g. for centWave not performed on that.

The new parameters expandMz, expandRt and ppm allow to increase the area (in m/z, retention time using absolute or relative values) from which the signal is integrated. This is a new feature that was not present in the old fillPeaks.

[lecorguille]

@jotsetung Thanks!
According to you, expandMz, expandRt and ppm are some basic parameters or advanced ones?
In other words, should the users think about those parameters or the default values suit at 90%?

[lecorguille]

Done 7dda1f5
Thanks again @jotsetung