API for MeenaChoi/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 |
| MSstatsSummarizeWithMultipleCores | Man page Source code |
| MSstatsSummarizeWithSingleCore | 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 |
| example_SDRF | Man page |
| 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 |
| groupComparisonQCPlots | 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 |
| validateAnnotation | Man page Source code |
