feat: add new `filterPeaksRanges` function

rformassspectrometry / Spectra

Low level infrastructure to handle MS spectra

https://rformassspectrometry.github.io/Spectra/

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feat: add new `filterPeaksRanges` function #326

Closed jorainer closed 4 months ago

jorainer commented 4 months ago

Add a new filterPeaksRanges function that allows to filter mass peaks in a Spectra by any (combination of) numeric spectra and peaks variables.
Re-organize documentation of filter and subset operations (related to issue #288).

jorainer commented 4 months ago

A nice use case for this function would be to filter a LC-MS data set keeping (or removing) all mass peaks that were considered a chromatographic peak by xcms-based preprocessing. This allows e.g. to evaluate the foreground (i.e. all quantified ion signal) and background signal (i.e. background noise, or signal that was not considered a valid chromatographic peak by xcms) of a full data set.

I will later add such a use case to the xcmsTutorials tutorial/workshop.

jorainer commented 4 months ago

Thanks @philouail ! I addressed all of your points! Hope documentation is now a bit clearer. Happy for additional/extra feedback, otherwise I proceed and merge tomorrow.