Added extended findPeaks function

[Treutler]

No description provided.

[jorainer]

Some comments here:

1. Is there a need to add these new parameters at all? They are not needed by your new findPeaks method.
2. Rename perform1stBaselineCheck to firstBaselineCheck.
3. You should perform some input argument checking, i.e. that length roiScales matches length of ROI.list and that roiScales contains numeric values.
4. Most importantly however: document the new arguments in the corresponding Rd file.

[jorainer]

Dear Hendrik, first of all, thanks for your contribution!

General comment (summarizing the above notes):

• I would put the logic of the second step (adding isotope peaks) into its own function.
• A detailed documentation of the method is missing: this should contain also motivation, expected results and description of all parameters.
• I strongly suggest to use individual parameters instead of passing a list with options as a parameter (i.e. the addROIsParams).

[sneumann]

* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'findPeaks.addPredictedIsotopeFeatures-methods.Rd':
  ‘findPeaks.centWave-methods’

Missing link or links in documentation object 'findPeaks.centWaveWithPredictedIsotopeROIs-methods.Rd':
  ‘findPeaks.addPredictedIsotopeFeatures-methods’
  ‘findPeaks.centWave-methods’

See section 'Cross-references' in the 'Writing R Extensions' manual.

[sneumann]

Hi @HendrikTreutler , this still has issues

* checking Rd metadata ... WARNING
Rd files with duplicated alias 'findPeaks.addPredictedIsotopeFeatures':
  ‘findPeaks.addPredictedIsotopeFeatures-methods.Rd’
  ‘findPeaks.centWaveWithPredictedIsotopeROIs-methods.Rd’
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'findPeaks.centWaveWithPredictedIsotopeROIs' and siglist
    'xcmsRaw'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.