Johannes Rainer

Also here a more general comment: would it not be possible to add information on the modifications directly as peaks/spectra variables to the `Spectra` object? the `labels` function for `plotSpectra()`...

Perfect! thanks! I let you the honor of merging and pushing to Bioconductor ;) (ideally to both, the RELEASE_3_22 and the devel branches)

Which version of *xcms* are you using? Ideally, post the output from `sessionInfo()` here. What you could try is to use `suppressMessages(chromatogram... )` . Another suggestion - it can be...

Actually, at present, we only have the `filterChromPeaks()` function that takes the indices of the chrom peaks to keep (parameter `keep`). So, you would need to use the `chromPeakSummary()` first,...

WOW, thanks @melpetera for the thorough investigation and description of the problem! I have two suggestions: 1) would be great if you could provide a reproducible example - ideally using...

Hi, thanks for reporting back and no worries - I did not mean to put pressure on you. it's also perfectly fine to report, thanks!

I had a look at your example, thanks for providing that. Just so that I understand it correctly - the main issue I see is that `minFraction` does only consider...

yes, thanks for the update @melpetera - I also added now a unit test to cover this, and `groupChromPeaks()` works as expected - only the `plotChromPeakDensity(... , simulate = TRUE)`...

I can confirm that your suggestions above work, i.e., the `unique()` call and incrementing `snum` in the `while`. I will include these fixes in the next version. Thanks @melpetera !

Thanks for the feedback @JohanLassen . yes, I agree, there is overlap. This was also just an idea - but of course, we should rather focus on *MsFeatures* and implement...