checkRepeatedDesign     Check if data represents repeated measurements
                        design
dataProcess             Process MS data: clean, normalize and summarize
                        before differential analysis
dataProcessPlots        Visualization for explanatory data analysis
DDARawData              Example dataset from a label-free DDA, a
                        controlled spike-in experiment.
DDARawData.Skyline      Example dataset from a label-free DDA, a
                        controlled spike-in experiment, processed by
                        Skyline.
designSampleSize        Planning future experimental designs of
                        Selected Reaction Monitoring (SRM),
                        Data-Dependent Acquisition (DDA or shotgun),
                        and Data-Independent Acquisition (DIA or
                        SWATH-MS) experiments in sample size
                        calculation
designSampleSizePlots   Visualization for sample size calculation
DIARawData              Example dataset from a label-free DIA, a group
                        comparison study of S.Pyogenes.
example_SDRF            Example SDRF.
extractSDRF             Extract experimental design from MSstats format
                        into SDRF format
getProcessed            Get feature-level data to be used in the
                        MSstatsSummarizationOutput function
getSamplesInfo          Get information about number of measurements
                        for each group
getSelectedProteins     Get proteins based on names or integer IDs
groupComparison         Whole plot testing
groupComparisonPlots    Visualization for model-based analysis and
                        summarizing differentially abundant proteins
groupComparisonQCPlots
                        Visualization for model-based quality control
                        in fitting model
makePeptidesDictionary
                        Prepare a peptides dictionary for global
                        standards normalization
modelBasedQCPlots       Visualization for model-based quality control
                        in fitting model
MSstatsContrastMatrix   Create a contrast matrix for groupComparison
                        function
MSstatsGroupComparison
                        Group comparison
MSstatsGroupComparisonOutput
                        Create output of group comparison based on
                        results for individual proteins
MSstatsGroupComparisonSingleProtein
                        Group comparison for a single protein
MSstatsHandleMissing    Handle censored missing values
MSstatsMergeFractions   Re-format the data before feature selection
MSstatsNormalize        Normalize MS data
MSstatsPrepareForDataProcess
                        Prepare data for processing by 'dataProcess'
                        function
MSstatsPrepareForGroupComparison
                        Prepare output for dataProcess for group
                        comparison
MSstatsPrepareForSummarization
                        Prepare feature-level data for protein-level
                        summarization
MSstatsQualityMetricsPlot
                        Plot quality metrics from converter output
MSstatsSelectFeatures   Feature selection before feature-level data
                        summarization
MSstatsSummarizationOutput
                        Post-processing output from MSstats
                        summarization
MSstatsSummarizeSingleLinear
                        Linear model-based summarization for a single
                        protein
MSstatsSummarizeSingleTMP
                        Tukey Median Polish summarization for a single
                        protein
MSstatsSummarizeWithMultipleCores
                        Feature-level data summarization with multiple
                        cores
MSstatsSummarizeWithSingleCore
                        Feature-level data summarization with 1 core
quantification          Protein sample quantification or group
                        quantification
savePlot                Save a plot to pdf file
SDRFtoAnnotation        Convert SDRF experimental design file into an
                        MSstats annotation file
SRMRawData              Example dataset from a SRM experiment with
                        stable isotope labeled reference of a time
                        course yeast study
theme_msstats           Theme for MSstats plots
validateAnnotation      Check if annotation matches intended
                        experimental design
