Man pages for eahrne/SafeQuant
A Toolbox for the Analysis of Proteomics Data

addIdQvaluesAdd identification leve q-values to ExpressionSet (calculated...
addScaffoldPTMFAnnotationsAdd scaffold ptm annotaitons to tmt experiment
barplotMSSignalBarplot of ms-signal per column
COLORScolor vector
createExpDesignCreate Experimental Design
createExpressionDatasetCreate ExpressionSet object
createPairedExpDesignCreate Paired Expdesign
cvBoxplotC.V. boxplot
cysteinFreqBarplotPlot Cystein Frequency
dotProductReturn dotProduct of two vectors
expDesignTagToExpDesignCreate experimental design data.frame from user input string
exportExport content of safeQuantAnalysis object
getAAProteinCoordinatesGet amino acid coordinates on protein
getAccessionNumberExtract accession numbers from Uniprot proteinNames
getAllCVCalculate Coefficiant of Variance per feature (Relative...
getAllDotProductReturn dotProducts to most transition intensities of most...
getAllEBayesPerform statistical test (mderated t-test), comparing all...
getBaselineIntensityGet signal at zscore x (x standard deviations below mean)
getCVCalculate Coefficiant of Variance per feature (Relative...
getExpDesignProgenesisCsvParse Experimental Design from Progenesis Csv Export
getFTestPValuePerform statistical test (mderated F-test)
getGeneNameExtract Gene Name from uniprot fasta header description
getGlobalNormFactorsGet normalization factors. calculated as summed/median signal...
getGoTermDFGet Go term data for a list of uniprot accession numbers
getIBAQEsetCalculate intensity-based absolute-protein-quantification...
getIdLevelQvalsCalculates identification level q-values based on...
getImpuritiesMatrixGet Thermo TMT impurity matrix
getImputationMatrixGet matrix of imputed valeus in ExpressionSet matrix
getIntSumPerProteinSum up raw intensities per protein and channel. keep track of...
getKinaseFreqGet kinase matching frequnecy of each phospho peptide...
getKinasesGet all kinases matching phospho peptide sub sequnece
getLODReturn dilution curve limit of detection
getLoocvFoldErrorLeave-One-Out Cross Validate Qunatification Model
getMaxIndexget index of max in vecotor of numeric values
getMeanCenteredRangeGet modification coordinates on protein
getModifProteinCoordinatesGet modification coordinates on protein
getMotifFreqGet motif matching frequnecy of each phospho peptide...
getMotifXCreate motif-x peptide annotation
getNAFractionGet fraction missing values per ratio/condition/run
getNbDetectablePeptidesGet number peptides passing defined length criteria
getNbMisCleavagesGet number of mis-cleavages perp peptide
getNbPeptidesPerProteinGet number of peptides per protein
getNbRolledUpFeaturesGet number rolled up features per row
getNbSpectraPerProteinGet number of spectra per protein
getPeptidesDigest protein
getRatiosCalculate ratios, comparing all case to control
getRTNormFactorsGet retentiontime base normalization factors
getScoreCutOffGet score cutoff for a given fdr cut-off
getSignalPerConditionSummarize replicate signal per condition (min)
getSwathsget swath sizes ensuring equal number of precurosrs per swath
getTopXCalculate Mean of X most intense features
getUserOptionsRead User Specified Command Line Options
ggDilutionCurvePlot dilution curve
ggVolcanoPlotPlots volcano, data points colored by max cv of the 2...
globalNormalizeNormalize, Norm factors calculated as median signal per run...
hClustHeatMapHierarchical clustering heat map, cluster by pearson...
hClustHeatMapOldHierarchical clustering heat map, cluster by runs intensity,...
isConCheck if protein is a contaminant entry
isDecoyCheck if protein is a decoy entry
isStrippedACsCheck if ACs are in "non-stripped" uniprot format e.g....
kinaseMotifKinase motifs
missinValueBarplotPlot Percentage of Features with with missing values
option_listCommand Line Option List
pairsAnnotPlot lower triangle Pearsons R^2. Diagonal text, upper...
parseMaxQuantProteinGroupTxtParse MaxQuant Protein Group Txt
parseProgenesisFeatureCsvParse Progenesis Feature Csv Export
parseProgenesisPeptideMeasurementCsvParse Progenesis Peptide Measurement Csv Export
parseProgenesisProteinCsvParse Progenesis Protein Csv
parseScaffoldPTMReportParse scaffold PTM Spectrum Report
parseScaffoldRawFileParse scaffold output .xls file (RAW export)
perFeatureNormalizationPer Feature Normalization
plotAbsEstCalibrationCurvePlot absolut Estimation calibration Curve
plotAdjustedVsNonAdjustedRatioPlot adjusted tmt ratios vs original ratios
plotAllGGVolcanoesPlots volcano of all condition comparisons
plotExpDesignDisplay experimental design, high-lighting the control...
plotIdScoreVsFDRPlot FDR vs. identification score
plotLogoPlot sequence logo
plotMSSignalDistributionsPlot ms.signal distributions
plotNbIdentificationsVsRTPlot the number of identified Features per Reteintion Time...
plotNbValidDeFeaturesPerFDRPlot Total Number of diffrentially Abundant Features...
plotPrecMassErrorDistribPlot Precursor Mass Error Distribution
plotPrecMassErrorVsScorePlot precursorMass error v.s score highlighting decoy and...
plotQValueVsPValuePlot qValue vs pValue
plotROCPlot Number of Identifications vs. FDR
plotRTNormPlot all retention time profile overalying ratios
plotRTNormSummaryPlot all retention time normalization profiles
plotScoreDistribPlot identifications target decoy distribution
plotVolcanoPlots volcano, data points colored by max cv of the 2...
plotXYDensityScatter plot with density coloring
purityCorrectTMTCorrect channel intensities based on Reporter ion Isotopic...
removeOutliersSet value to NA if it deviatves with more than 1.5 * IQR from...
rollUpRoll up feature intensites per unique colum combination
rollUpDTRoll up feature intensites per unique colum combination
rtNormalizeNormalization data per retention time bin
safeQuantAnalysissafeQunat s3 class
setNbPeptidesPerProteinSet nbPeptides coulmn of featureData
setNbSpectraPerProteinSet nbPeptides coulmn of featureData
sqImputeImpute missing values
stripACsstrip uniprot format e.g. "sp|Q8CHJ2|AQP12_MOUSE" -> Q8CHJ2
eahrne/SafeQuant documentation built on Feb. 22, 2018, 12:05 p.m.