This function selects the columns from the standard OpenSWATH output to column needed for MSstats, aLFQ and mapDIA.
reduce_OpenSWATH_output(data, column.names = NULL)A data frame containing SWATH data.
A vector of column names that can be selected.
Returns a data frame with the selected columns.
A basic set of columns are defined in the function and are used if no column names are indicated.
The column.names can be omitted and then the following columns are selected that are needed for MSstats and mapDIA analysis: ProteinName, FullPeptideName, Sequence, Charge, aggr_Fragment_Annotation, aggr_Peak_Area, filename, m_score, decoy, Intensity, RT. This function should be ommitted if the data is analyzed afterwards with the aLFQ or imsbInfer package that needs further columns.
data("OpenSWATH_data", package="SWATH2stats")
data("Study_design", package="SWATH2stats")
data <- sample_annotation(OpenSWATH_data, Study_design)
data.filtered <- reduce_OpenSWATH_output(data)