return EIC with peak detection output

[cbroeckl]

possible feature request. I find myself wanting EIC chromatograms for detected peaks with some regularity, for different reasons. Going back and getting the EIC values for each feature is (relatively) slow after peak detection. It would seem to me it would be fastest to return the EIC as peak detection is occurring, since all of the relevant raw data is in memory at that point. would it be possible to (optionally) return the EIC for each detected peak at the peak detection (and possible the fillPeaks) stage? The output size of the xcms object will of course be somewhat larger, maybe this becomes prohibitive? Not urgent, but a potentially useful output addition which keeps computational time down.

[jorainer]

Thanks for the suggestion. Adding/caching detected peaks during the peak detection step would require quite some internal changes - but it's something I will definitely keep in mind (since we're planning to improve chromatographic data support in future).

What you could however do is to use the featureChromatograms function or (in the current developmental version) the chromPeakChromatograms functions - that should simplify the extraction. Also, the newer versions (in the developmental xcms version) should be faster.

Maybe have a look at the new workflow/classes that will be introduced with this new version (getting released end of October): https://sneumann.github.io/xcms/articles/xcms.html - we're now also supporting directly the newer MsExperiment and Spectra packages. This should help speed up things and also have more possibilities (such as loading the full data into memory, keeping the data in a SQL database, ...).