COLORS                  color vector
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
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
getRTNormFactors        Get retentiontime base normalization factors
getRatios               Calculate ratios, comparing all case to control
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
