Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

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Documentation for package ‘MSstatsConvert’ version 1.19.3

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.cleanRawPD Clean raw Proteome Discoverer data
as.data.frame.MSstatsValidated Convert output of converters to data.frame
as.data.table.MSstatsValidated Convert output of converters to data.table
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
getInputFile Get one of files contained in an instance of 'MSstatsInputFiles' class.
getInputFile-method Get one of files contained in an instance of 'MSstatsInputFiles' class.
MaxQtoMSstatsFormat Import MaxQuant files
MetamorpheusToMSstatsFormat Import Metamorpheus 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.
MSstatsClean-method 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
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