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fgcz / rawrr

Access Orbitrap data in R lang using C# mono assembly - bioconductor package
https://bioconductor.org/packages/rawrr/
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Request for auc.rawrrChromatogram #68

Open rolivella opened 1 year ago

rolivella commented 1 year ago

Hello!

I would like to suggest a little bit more informative output for rawrr:::auc.rawrrChromatogram fucntion. For instance with observed RT and mz, something like: 

XIC generated from 20230525_QCN1_001_03.raw consisting of 1454 data points.
   Filter : ms
   m/z : 259.0925
   m/z obs: 259.0889
   RT obs: 12.4 min
   Tolerance : 10 ppm
   RT : 0.001045075 - 41.0016 min
[1] 159020992

By "obs" I mean the RT and mz where the rawrr:::auc.rawrrChromatogram fucntion found the peak for integrating the area.

This will be very useful for us and in general for any rawrr user.

Thanks!

tobiasko commented 1 year ago

To my knowledge rawrr:::auc.rawrrChromatogram returns the integral with f(x) being the chromatogram. It is not a peak picker. Accordingly, the return value of the function is a real value.

rolivella commented 1 year ago

Maybe you can compute the local maximum as a measure of the observed RT and mz

tobiasko commented 1 year ago

The m/z is set by readChromatogram and its parameters. Again, the auc. function is not a peak caller, it just integrates. There is general R functions to retrieve global and local maxima (inflection points).