Johannes Rainer

You can not take this parameter as a *hard cutoff* for peaks. In fact, *centWave* selects based on this parameter different scales for the continuous wavelet transform. I usually select...

I'm a little puzzled by the very few datapoints you have in the `plot(... , type = "XIC")` above. There it looks like you have a single high intensity signal...

Can you please provide a PR with the suggested changes?

If I got you right, you have an experiment with some files that contain only MS1 data and some files with MS1 and MS2 data? In such cases `xcms` will...

Note: a second solution would be to use `return.type = "Spectra"` or `return.type = "List"`. In both cases the function should work on the full data set.

And if you want to run this without parallel processing simply call it with `adjustRtime(..., BPPARAM = SerialParam()` or alternatively (to disable parallel processing for all `xcms` functions: ```r register(SerialParam())...

Could you also try to do a `data

I've added a tentative fix that should at least avoid the error that is thrown. Can you please install that with `devtools::install_github("sneumann/xcms", ref = "jomaster")` and try again? Also, seems...

What surprises me is that you don't have continuous retention times (e.g. for the first file `0.51, 0.56` but then it jumps to `2.59, 2.66` and then again to `3.33`)....

I guess alignment should be possible. The problem is that there is this limitation in the `xcms` code to *cut* the data if it finds gaps in retention times -...