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| addIdQvalues | Add identification leve q-values to ExpressionSet (calculated based on target-decoy score distribution) |
| addScaffoldPTMFAnnotations | Add scaffold ptm annotaitons to tmt experiment |
| barplotMSSignal | Barplot of ms-signal per column |
| COLORS | color vector |
| createExpDesign | Create Experimental Design |
| createExpressionDataset | Create ExpressionSet object |
| createPairedExpDesign | Create Paired Expdesign |
| cvBoxplot | C.V. boxplot |
| expDesignTagToExpDesign | Create experimental design data.frame from user input string |
| export | Export content of safeQuantAnalysis object |
| getAAProteinCoordinates | Get amino acid coordinates on protein |
| getAllCV | Calculate Coefficiant of Variance per feature (Relative standard Deviation) per Condition |
| getAllEBayes | Perform statistical test (mderated t-test), comparing all case to control |
| getBaselineIntensity | Get signal at zscore x (x standard deviations below mean) |
| getCV | Calculate Coefficiant of Variance per feature (Relative standard Deviation) |
| getExpDesignProgenesisCsv | Parse Experimental Design from Progenesis Csv Export |
| getGlobalNormFactors | Get normalization factors. calculated as summed/median signal per run (column) over summed/median of first run. |
| getIBAQEset | Calculate intensity-based absolute-protein-quantification (iBAQ) metric per protein |
| getIdLevelQvals | Calculates identification level q-values based on target-decoy score distributions |
| getImpuritiesMatrix | Get Thermo TMT impurity matrix |
| getIntSumPerProtein | Sum up raw intensities per protein and channel. keep track of number of summed spectra and unique peptides |
| getLoocvFoldError | Leave-One-Out Cross Validate Qunatification Model |
| getMaxIndex | get index of max in vecotr of numeric values |
| getMeanCenteredRange | Get modification coordinates on protein |
| getModifProteinCoordinates | Get modification coordinates on protein |
| getMotifX | Create motif-x peptide annotation |
| getNbDetectablePeptides | Get number peptides passing defined length criteria |
| getNbMisCleavages | Get number of mis-cleavages perp peptide |
| getNbPeptidesPerProtein | Get number of peptides per protein |
| getNbSpectraPerProtein | Get number of spectra per protein |
| getPeptides | Digest protein |
| getRatios | Calculate ratios, comparing all case to control |
| getRTNormFactors | Get retentiontime base normalization factors |
| getScoreCutOff | Get score cutoff for a given fdr cut-off |
| getSignalPerCondition | Summarize replicate signal per condition (min) |
| getTopX | Calculate Mean of X most intense features |
| getUserOptions | Read User Specified Command Line Options |
| globalNormalize | Normalize, Norm factors calculated as median signal per run (column) over median of first run. |
| hClustHeatMap | Hierarchical clustering heat map, cluster by runs intensity, features by ratio and display log2 ratios to control median |
| isCon | Check if protein is a contaminant entry |
| isDecoy | Check if protein is a decoy entry |
| isStrippedACs | Check if ACs are in "non-stripped" uniprot format e.g. "sp|Q8CHJ2|AQP12_MOUSE" |
| maPlotSQ | ma-plot |
| missinValueBarplot | Plot Percentage of Features with with missing values |
| option_list | Command Line Option List |
| pairsAnnot | Plot lower triangle Pearsons R^2. Diagonal text, upper triangle all against all scatter plots with lm abline |
| parseMaxQuantProteinGroupTxt | Parse MaxQuant Protein Group Txt |
| parseProgenesisFeatureCsv | Parse Progenesis Feature Csv Export |
| parseProgenesisPeptideMeasurementCsv | Parse Progenesis Peptide Measurement Csv Export |
| parseProgenesisProteinCsv | Parse Progenesis Protein Csv |
| parseScaffoldPTMReport | Parse scaffold PTM Spectrum Report |
| parseScaffoldRawFile | Parse scaffold output .xls file (RAW export) |
| perFeatureNormalization | Per Feature Normalization |
| plotAbsEstCalibrationCurve | Plot absolut Estimation calibration Curve |
| plotAdjustedVsNonAdjustedRatio | Plot adjusted tmt ratios vs original ratios |
| plotExpDesign | Display experimental design, high-lighting the control condition |
| plotIdScoreVsFDR | Plot FDR vs. identification score |
| plotMSSignalDistributions | Plot ms.signal distributions |
| plotNbIdentificationsVsRT | Plot the number of identified Features per Reteintion Time minute. |
| plotNbValidDeFeaturesPerFDR | Plot Total Number of diffrentially Abundant Features (applying ratio cutoff) vs. qValue/pValue for all conditions |
| plotPrecMassErrorDistrib | Plot Precursor Mass Error Distribution |
| plotPrecMassErrorVsScore | Plot precursorMass error v.s score highlighting decoy and displaying user specified user specified precursor mass filter |
| plotQValueVsPValue | Plot qValue vs pValue |
| plotROC | Plot Number of Identifications vs. FDR |
| plotRTNorm | Plot all retention time profile overalying ratios |
| plotRTNormSummary | Plot all retention time normalization profiles |
| plotScoreDistrib | Plot identifications target decoy distribution |
| plotVolcano | Plots volcano, data points colored by max cv of the 2 compared conditions |
| plotXYDensity | Scatter plot with density coloring |
| purityCorrectTMT | Correct channel intensities based on Reporter ion Isotopic Distributions |
| removeOutliers | Set value to NA if it deviatves with more than 1.5 * IQR from lower/upper quantile |
| rollUp | Roll up feature intensites per unique colum combination |
| rtNormalize | Normalization data per retention time bin |
| safeQuantAnalysis | safeQunat s3 class |
| setNbPeptidesPerProtein | Set nbPeptides coulmn of featureData |
| setNbSpectraPerProtein | Set nbPeptides coulmn of featureData |
| sqNormalize | Normalize |
| standardise | Standardise data |
| stripACs | strip uniprot format e.g. "sp|Q8CHJ2|AQP12_MOUSE" -> Q8CHJ2 |