If the SWATH data should be analyzed on transition-level the data needs to be tranformed from peptide-level table to a transition-level table (one row per transition instead of one row per peptide). The columns "aggr_Fragment_Annotation" and "aggr_Peak_Area" are disaggregated into the new columns "Fragmentation" and "Intensity". The following columns are renamed if they exist: FullPeptideName -> PeptideSequence, Charge -> PrecursorCharge, Area -> Intensity, Fragment -> Fragmentation, Sequence -> NakedSequence.
A data frame containing SWATH data.
Option that all columns are processed. Otherwise only the columns typically needed for downstream analysis are processed.
Returns a data frame containing the SWATH data in a transition-level table.
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