API for eahrne/SafeQuant
A Toolbox for the Analysis of Proteomics Data
| Global functions | |
|---|---|
| .addPTMCoord | Source code |
| .allpValueHist | Source code |
| .correlationPlot | Source code |
| .dotColorstrip | Source code |
| .errorBar | Source code |
| .exp2Exprs | Source code |
| .filterSQA | Source code |
| .getCalibMixEset | Source code |
| .getCalibMixPairedEset | Source code |
| .getConditionColors | Source code |
| .getControlCondition | Source code |
| .getFileType | Source code |
| .getFirstEntry | Source code |
| .getNbPlex | Source code |
| .getProgenesisCsvExpressionColIndices | Source code |
| .getProteaseRegExp | Source code |
| .getSkipLineNb | Source code |
| .getUniquePtmMotifs | Source code |
| .idOverviewPlots | Source code |
| .idPlots | Source code |
| .intensityAdjustment | Source code |
| .log2Exprs | Source code |
| .outerLegend | Source code |
| .plotVolcano | Source code |
| .qcPlots | Source code |
| .setFilter | Source code |
| COLORS | Man page |
| addIdQvalues | Man page Source code |
| addScaffoldPTMFAnnotations | Man page Source code |
| barplotMSSignal | Man page |
| createExpDesign | Man page Source code |
| createExpressionDataset | Man page Source code |
| createPairedExpDesign | Man page Source code |
| cvBoxplot | Man page |
| cysteinFreqBarplot | Man page |
| dotProduct | Man page Source code |
| expDesignTagToExpDesign | Man page Source code |
| export | Man page Source code |
| getAAProteinCoordinates | Man page Source code |
| getAccessionNumber | Man page |
| getAllCV | Man page Source code |
| getAllDotProduct | Man page Source code |
| getAllEBayes | Man page Source code |
| getBaselineIntensity | Man page Source code |
| getCV | Man page Source code |
| getExpDesignProgenesisCsv | Man page Source code |
| getFTestPValue | Man page Source code |
| getGeneName | Man page |
| getGlobalNormFactors | Man page Source code |
| getGoTermDF | Man page |
| getIBAQEset | Man page Source code |
| getIdLevelQvals | Man page Source code |
| getImpuritiesMatrix | Man page |
| getImputationMatrix | Man page |
| getIntSumPerProtein | Man page Source code |
| getKinaseFreq | Man page Source code |
| getKinases | Man page Source code |
| getLOD | Man page Source code |
| getLoocvFoldError | Man page Source code |
| getMaxIndex | Man page Source code |
| getMeanCenteredRange | Man page Source code |
| getModifProteinCoordinates | Man page Source code |
| getMotifFreq | Man page Source code |
| getMotifX | Man page Source code |
| getNAFraction | Man page |
| getNbDetectablePeptides | Man page Source code |
| getNbMisCleavages | Man page Source code |
| getNbPeptidesPerProtein | Man page Source code |
| getNbRolledUpFeatures | Man page |
| getNbSpectraPerProtein | Man page Source code |
| getPeptides | Man page Source code |
| getRTNormFactors | Man page Source code |
| getRatios | Man page Source code |
| getScoreCutOff | Man page Source code |
| getSignalPerCondition | Man page Source code |
| getSwaths | Man page Source code |
| getTopX | Man page Source code |
| getUserOptions | Man page Source code |
| ggDilutionCurve | Man page Source code |
| ggVolcanoPlot | Man page Source code |
| globalNormalize | Man page Source code |
| hClustHeatMap | Man page |
| hClustHeatMapOld | Man page |
| isCon | Man page Source code |
| isDecoy | Man page Source code |
| isStrippedACs | Man page Source code |
| kinaseMotif | Man page |
| maPlotSQ | Man page |
| missinValueBarplot | Man page |
| option_list | Man page |
| pairsAnnot | Man page |
| parseCSV | Source code |
| parseMaxQuantProteinGroupTxt | Man page Source code |
| parseProgenesisFeatureCsv | Man page Source code |
| parseProgenesisPeptideMeasurementCsv | Man page Source code |
| parseProgenesisProteinCsv | Man page Source code |
| parseScaffoldPTMReport | Man page Source code |
| parseScaffoldRawFile | Man page Source code |
| perFeatureNormalization | Man page Source code |
| plot.safeQuantAnalysis | Source code |
| plotAbsEstCalibrationCurve | Man page |
| plotAdjustedVsNonAdjustedRatio | Man page |
| plotAllGGVolcanoes | Man page Source code |
| plotExpDesign | Man page Source code |
| plotIdScoreVsFDR | Man page |
| plotLogo | Man page |
| plotMSSignalDistributions | Man page |
| plotNbIdentificationsVsRT | Man page |
| plotNbValidDeFeaturesPerFDR | Man page |
| plotPrecMassErrorDistrib | Man page |
| plotPrecMassErrorVsScore | Man page |
| plotQValueVsPValue | Man page |
| plotROC | Man page |
| plotRTNorm | Man page |
| plotRTNormSummary | Man page |
| plotScoreDistrib | Man page |
| plotVolcano | Man page Source code |
| plotXYDensity | Man page |
| print.safeQuantAnalysis | Source code |
| purityCorrectTMT | Man page Source code |
| removeOutliers | Man page Source code |
| rollUp | Man page Source code |
| rollUpDT | Man page Source code |
| rtNormalize | Man page Source code |
| safeQuantAnalysis | Man page Source code |
| setNbPeptidesPerProtein | Man page Source code |
| setNbSpectraPerProtein | Man page Source code |
| sqImpute | Man page |
| sqNormalize | Man page Source code |
| stripACs | Man page Source code |
