All functions
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DDARawData
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Example dataset from a label-free DDA, a controlled spike-in experiment. |
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DDARawData.Skyline
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Example dataset from a label-free DDA, a controlled spike-in experiment, processed by Skyline. |
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DIARawData
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Example dataset from a label-free DIA, a group comparison study of S.Pyogenes. |
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DIAUmpiretoMSstatsFormat()
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Import DIA-Umpire files |
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MSstatsContrastMatrix()
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Create a contrast matrix for groupComparison function |
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MSstatsGroupComparison()
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Group comparison |
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MSstatsGroupComparisonOutput()
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Create output of group comparison based on results for individual proteins |
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MSstatsGroupComparisonSingleProtein()
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Group comparison for a single protein |
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MSstatsHandleMissing()
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Handle censored missing values |
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MSstatsMergeFractions()
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Re-format the data before feature selection |
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MSstatsNormalize()
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Normalize MS data |
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MSstatsPrepareForDataProcess()
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Prepare data for processing by `dataProcess` function |
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MSstatsPrepareForGroupComparison()
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Prepare output for dataProcess for group comparison |
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MSstatsPrepareForSummarization()
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Prepare feature-level data for protein-level summarization |
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MSstatsSelectFeatures()
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Feature selection before feature-level data summarization |
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MSstatsSummarizationOutput()
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Post-processing output from MSstats summarization |
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MSstatsSummarize()
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Feature-level data summarization |
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MSstatsSummarizeSingleLinear()
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Linear model-based summarization for a single protein |
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MSstatsSummarizeSingleTMP()
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Tukey Median Polish summarization for a single protein |
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MaxQtoMSstatsFormat()
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Import MaxQuant files |
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OpenMStoMSstatsFormat()
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Import OpenMS files |
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OpenSWATHtoMSstatsFormat()
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Import OpenSWATH files |
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PDtoMSstatsFormat()
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Import Proteome Discoverer files |
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ProgenesistoMSstatsFormat()
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Import Progenesis files |
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SRMRawData
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Example dataset from a SRM experiment with stable isotope labeled reference of a time course yeast study |
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SkylinetoMSstatsFormat()
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Import Skyline files |
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SpectronauttoMSstatsFormat()
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Import Spectronaut files |
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checkRepeatedDesign()
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Check if data represents repeated measurements design |
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dataProcess()
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Process MS data: clean, normalize and summarize before differential analysis |
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dataProcessPlots()
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Visualization for explanatory data analysis |
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designSampleSize()
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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 |
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designSampleSizePlots()
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Visualization for sample size calculation |
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getProcessed()
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Get feature-level data to be used in the MSstatsSummarizationOutput function |
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getSamplesInfo()
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Get information about number of measurements for each group |
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getSelectedProteins()
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Get proteins based on names or integer IDs |
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groupComparison()
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Whole plot testing |
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groupComparisonPlots()
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Visualization for model-based analysis and summarizing differentially abundant proteins |
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makePeptidesDictionary()
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Prepare a peptides dictionary for global standards normalization |
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modelBasedQCPlots()
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Visualization for model-based quality control in fitting model |
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quantification()
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Protein sample quantification or group quantification |
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savePlot()
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Save a plot to pdf file |
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theme_msstats()
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Theme for MSstats plots |