.cleanRawPD             Clean raw Proteome Discoverer data
.validatePDTMTInputColumns
                        Helper method to validate input has necessary
                        columns
DIANNtoMSstatsFormat    Import Diann files
DIAUmpiretoMSstatsFormat
                        Import DIA-Umpire files
FragPipetoMSstatsFormat
                        Import FragPipe files
MSstatsBalancedDesign   Creates balanced design by removing overlapping
                        fractions and filling incomplete rows
MSstatsClean            Clean files generated by a signal processing
                        tools.
MSstatsConvert          MSstatsConvert: An R Package to Convert Data
                        from Mass Spectrometry Signal Processing Tools
                        to MSstats Format
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
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.
