disaggregate {SWATH2stats} | R Documentation |
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 "FragmentIon" and "Intensity". The following columns are renamed if they exist: FullPeptideName -> PeptideSequence, Charge -> PrecursorCharge, Area -> Intensity, Fragment -> FragmentIon, Sequence -> NakedSequence.
disaggregate(data, all.columns = FALSE)
data |
A data frame containing SWATH data. |
all.columns |
Option that all columns are processed. Otherwise only the typical columns needed for downstream analysis are processed. |
Returns a data frame containing the SWATH data in a transition-level table.
Peter Blattmann
data("OpenSWATH_data", package="SWATH2stats") data("Study_design", package="SWATH2stats") data <- sample_annotation(OpenSWATH_data, Study_design) data.filtered.decoy <- filter_mscore(data, 0.01) raw <- disaggregate(data.filtered.decoy)