Johannes Rainer

I suggest you start with installing all packages properly. These are Bioconductor packages, thus you should install them through Bioconductor (github installations are suggested only for more advanced users): ```r...

Please don't use `xcmsSet` and similar functionality (`group`...) anymore. This part of the `xcms` code is no longer maintained or fixed. The error message seems to be related to the...

The functions are in place. @michaelwitting if you want to test: `chromPeakSpectra` extracts MS2 spectra for chromatographic peaks, `featureSpectra` for features. Both return (at the moment) a `list` of `Spectrum2`...

I thought it would fit because it is a very general object (essentually just a `list` of `Spectrum` objects with arbitrary metadata information. Let's see - eventually I'll add to...

Everything is in place in the *ms2_spectra* branch (i.e. new `Spectra` object etc). Just waiting whether the class will not be included into `MSnbase` (could also be reused then in...

@michaelwitting please update `MSnbase` (from github) and `xcms` from the github master branch. `MSnbase` 2.7.8 has `Spectra` present and the `writeMgfData` function to export `Spectra` objects. I made also some...

I don't get an error anymore with `featureSpectra` with the new versions. Regarding the masses with zero intensities. Yes, indeed, there are a lot of 0 in the `Spectrum2` objects....

This is very strange. Can you please install `MSnbase` again from github? There is now a version 2.7.10. Also make sure you close R and start it again. You should...

BTW, an nicer solution to the intermediate approach `ms2_features@listData

Regarding selecting one Spectra per file and feature: you could either use the `method` parameter in `featureSpectra` to select the representative `Spectrum2`. I could also add a `method = "TIC"`...