API for Vitek-Lab/MSstats
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Global functions
.addCoverageInfo Man page Source code
.addModelInformation Man page Source code
.addModelVariances Man page Source code
.addNInformativeInfo Man page Source code
.addNoisyFlag Man page Source code
.addOutlierCutoff Man page Source code
.addOutlierInformation Man page Source code
.addSurvivalPredictions Man page Source code
.adjustLRuns Man page Source code
.calculateOutlierCutoff Man page Source code
.calculatePower Man page Source code
.calculateProteinVariance Man page Source code
.checkContrastMatrix Man page Source code
.checkDataProcessParams Man page Source code
.checkExperimentDesign Man page Source code
.checkGCPlotsInput Man page Source code
.checkGroupComparisonInput Man page Source code
.checkSingleFeature Man page Source code
.checkSingleLabelProteins Man page Source code
.checkSingleSubject Man page Source code
.checkTechReplicate Man page Source code
.checkUnProcessedDataValidity Man page Source code
.convertGgplot2Plotly Source code
.countInformative Man page Source code
.countMissingPercentage Man page Source code
.documentFunction Man page Source code
.finalizeInput Man page Source code
.finalizeLinear Man page Source code
.finalizeTMP Man page Source code
.fitHuber Man page Source code
.fitLinearModel Man page Source code
.fitModelForGroupComparison Man page Source code
.fitModelSingleProtein Man page Source code
.fitSurvival Source code
.fitTukey Man page Source code
.fixCensoredPointsLegendProfilePlotsPlotly Source code
.fixLegendPlotlyPlotsDataprocess Source code
.fixLegendPlotlyPlotsVolcano Source code
.flagLowCoverage Man page Source code
.flagUninformativeSingleLabel Man page Source code
.getAllComparisons Man page Source code
.getColorKeyGGPlot2 Man page Source code
.getColorKeyPlotly Man page Source code
.getContrast Man page Source code
.getContrastLabels Man page Source code
.getEmptyComparison Man page Source code
.getFeatureVariances Man page Source code
.getMedian Man page Source code
.getMedianSigmaSubject Man page Source code
.getMin Man page Source code
.getModelParameters Man page Source code
.getNonMissingFilter Man page Source code
.getNonMissingFilterStats Man page Source code
.getNumSample Man page Source code
.getOrderedMatrix Source code
.getPlotlyPlotHTML Source code
.getQuantileCutoff Source code
.getSingleProteinForProfile Man page Source code
.getVarComponent Man page Source code
.getWideTable Man page Source code
.getYaxis Man page Source code
.groupComparisonWithMultipleCores Man page Source code
.groupComparisonWithSingleCore Man page Source code
.handleEmptyConditions Man page Source code
.handleSingleContrast Man page Source code
.isSummarizable Man page Source code
.logDatasetInformation Man page Source code
.logMissingness Man page Source code
.logSingleLabeledProteins Man page Source code
.logSummaryStatistics Man page Source code
.makeComparison Man page Source code
.makeConditionPlot Man page Source code
.makeFactorColumns Man page Source code
.makeHeatmapGgplot2 Source code
.makeHeatmapPlotly Man page Source code
.makeProfilePlot Man page Source code
.makeQCPlot Man page Source code
.makeSummaryProfilePlot Man page Source code
.makeVolcano Man page Source code
.nicePrint Man page Source code
.normalizeGlobalStandards Man page Source code
.normalizeMedian Man page Source code
.normalizeQuantile Man page Source code
.onLoad Man page Source code
.plotComparison Man page Source code
.plotCondition Source code
.plotHeatmap Man page Source code
.plotProfile Source code
.plotQC Source code
.plotQQ Source code
.plotResiduals Source code
.plotVolcano Man page Source code
.preProcessIntensities Man page Source code
.prepareForDataProcess Man page Source code
.prepareLinear Man page Source code
.prepareSingleProteinForGC Man page Source code
.prepareSummary Man page Source code
.prepareTMP Man page Source code
.quantileNormalizationSingleLabel Man page Source code
.replaceZerosWithNA Man page Source code
.retainCensoredDataPoints Source code
.runTukey Man page Source code
.savePlotlyPlotHTML Source code
.saveSessionInfo Man page Source code
.saveTable Man page Source code
.selectHighQualityFeatures Man page Source code
.selectTopFeatures Man page Source code
.setCensoredByThreshold Man page Source code
.updateColumnsForProcessing Man page Source code
.updateUnequalVariances Man page Source code
DDARawData Man page
DDARawData.Skyline Man page
DIANNtoMSstatsFormat Man page Source code
DIARawData Man page
DIAUmpiretoMSstatsFormat Man page Source code
FragPipetoMSstatsFormat Man page Source code
MSstatsContrastMatrix Man page Source code
MSstatsContrastMatrix.character Source code
MSstatsContrastMatrix.data.frame Source code
MSstatsContrastMatrix.list Source code
MSstatsContrastMatrix.matrix Source code
MSstatsGroupComparison Man page Source code
MSstatsGroupComparisonOutput Man page Source code
MSstatsGroupComparisonSingleProtein Man page Source code
MSstatsHandleMissing Man page Source code
MSstatsMergeFractions Man page Source code
MSstatsNormalize Man page Source code
MSstatsPrepareForDataProcess Man page Source code
MSstatsPrepareForGroupComparison Man page Source code
MSstatsPrepareForSummarization Man page Source code
MSstatsSelectFeatures Man page Source code
MSstatsSummarizationOutput Man page Source code
MSstatsSummarize Man page Source code
MSstatsSummarizeSingleLinear Man page Source code
MSstatsSummarizeSingleTMP Man page Source code
MaxQtoMSstatsFormat Man page Source code
OpenMStoMSstatsFormat Man page Source code
OpenSWATHtoMSstatsFormat Man page Source code
PDtoMSstatsFormat Man page Source code
ProgenesistoMSstatsFormat Man page Source code
SDRFtoAnnotation Man page Source code
SRMRawData Man page
SkylinetoMSstatsFormat Man page Source code
SpectronauttoMSstatsFormat Man page Source code
checkRepeatedDesign Man page Source code
colMax Source code
colMin Source code
dataProcess Man page Source code
dataProcessPlots Man page Source code
designSampleSize Man page Source code
designSampleSizePlots Man page Source code
extractSDRF Man page Source code
getFileName Source code
getProcessed Man page Source code
getSamplesInfo Man page Source code
getSelectedProteins Man page Source code
get_estimable_fixed_random Source code
get_linear_summary Source code
groupComparison Man page Source code
groupComparisonPlots Man page Source code
makePeptidesDictionary Man page Source code
make_contrast_run_quant Source code
median_polish_summary Source code
modelBasedQCPlots Man page Source code
quantification Man page Source code
savePlot Man page Source code
theme_msstats Man page Source code
Vitek-Lab/MSstats documentation built on March 16, 2024, 7:48 p.m.