.cleanRawPD             Clean raw Proteome Discoverer data
CheckDataHealth         Takes as input the output of the
                        SpectronauttoMSstatsFormat function and
                        calculates various quality metrics to assess
                        the health of the data. Requires Anomaly
                        Detection model to be fit.
DIANNtoMSstatsFormat    Import Diann files
DIAUmpiretoMSstatsFormat
                        Import DIA-Umpire files
FragPipetoMSstatsFormat
                        Import FragPipe files
MSstatsAnomalyScores    Run Anomaly Model
MSstatsBalancedDesign   Creates balanced design by removing overlapping
                        fractions and filling incomplete rows
MSstatsClean            Clean files generated by a signal processing
                        tools.
MSstatsImport           Import files from signal processing tools.
MSstatsLogsSettings     Set how MSstats will log information from data
                        processing
MSstatsMakeAnnotation   Create annotation
MSstatsPreprocess       Preprocess outputs from MS signal processing
                        tools for analysis with MSstats
MSstatsSaveSessionInfo
                        Save session information
MaxQtoMSstatsFormat     Import MaxQuant files
MetamorpheusToMSstatsFormat
                        Import Metamorpheus files
OpenMStoMSstatsFormat   Import OpenMS files
OpenSWATHtoMSstatsFormat
                        Import OpenSWATH files
PDtoMSstatsFormat       Import Proteome Discoverer files
ProgenesistoMSstatsFormat
                        Import Progenesis files
ProteinProspectortoMSstatsTMTFormat
                        Generate MSstatsTMT required input format from
                        Protein Prospector output
SkylinetoMSstatsFormat
                        Import Skyline files
SpectronauttoMSstatsFormat
                        Import Spectronaut files
as.data.frame.MSstatsValidated
                        Convert output of converters to data.frame
as.data.table.MSstatsValidated
                        Convert output of converters to data.table
getInputFile            Get one of files contained in an instance of
                        'MSstatsInputFiles' class.
