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Two issues:
Plotting a CoreMS object where monoisotopic peaks and isotopic peaks identified different columns caused cbind of two different length vectors. Switched to a full join on the sample id column.
Conversion of CoreMSData to peakData had a step where the formulae were parsed assuming a static order of CHNOSP. Switched to using
ftmsRanalysis:::atom_count_vectorizer
on the CoreMS object's molecular formula column, which seems agnostic to oder.