Protein Significance Analysis in DDA, SRM and DIA for Label-free
or Label-based Proteomics Experiments
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Documentation for package ‘MSstats’ version 4.2.0
Help Pages
| 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. |
| DIAUmpiretoMSstatsFormat | Import DIA-Umpire files |
| 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 |
| makePeptidesDictionary | Prepare a peptides dictionary for global standards normalization |
| MaxQtoMSstatsFormat | Import MaxQuant files |
| 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 |
| MSstatsSelectFeatures | Feature selection before feature-level data summarization |
| MSstatsSummarizationOutput | Post-processing output from MSstats summarization |
| MSstatsSummarize | Feature-level data summarization |
| MSstatsSummarizeSingleLinear | Linear model-based summarization for a single protein |
| MSstatsSummarizeSingleTMP | Tukey Median Polish summarization for a single protein |
| OpenMStoMSstatsFormat | Import OpenMS files |
| OpenSWATHtoMSstatsFormat | Import OpenSWATH files |
| PDtoMSstatsFormat | Import Proteome Discoverer files |
| ProgenesistoMSstatsFormat | Import Progenesis files |
| quantification | Protein sample quantification or group quantification |
| savePlot | Save a plot to pdf file |
| SkylinetoMSstatsFormat | Import Skyline files |
| SpectronauttoMSstatsFormat | Import Spectronaut files |
| SRMRawData | Example dataset from a SRM experiment with stable isotope labeled reference of a time course yeast study |
| theme_msstats | Theme for MSstats plots |