SafeQuant: A Toolbox for the Analysis of Proteomics Data
Version 2.3.1

Tools for the statistical analysis and visualization of (relative and absolute) quantitative (LFQ,TMT,HRM) Proteomics data.

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AuthorErik Ahrne
Date of publication2016-12-06 14:04:35
MaintainerErik Ahrne <erik.ahrne@unibas.ch>
LicenseGPL-3
Version2.3.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SafeQuant")

Man pages

addIdQvalues: Add identification leve q-values to ExpressionSet (calculated...
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...
getAllEBayes: Perform statistical test (mderated t-test), comparing all...
getBaselineIntensity: Get signal at zscore x (x standard deviations below mean)
getCV: Calculate Coefficiant of Variance per feature (Relative...
getExpDesignProgenesisCsv: Parse Experimental Design from Progenesis Csv Export
getGlobalNormFactors: Get normalization factors. calculated as summed/median signal...
getIBAQEset: Calculate intensity-based absolute-protein-quantification...
getIdLevelQvals: Calculates identification level q-values based on...
getImpuritiesMatrix: Get Thermo TMT impurity matrix
getIntSumPerProtein: Sum up raw intensities per protein and channel. keep track of...
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...
hClustHeatMap: Hierarchical clustering heat map, cluster by runs intensity,...
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....
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...
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...
plotIdScoreVsFDR: Plot FDR vs. identification score
plotMSSignalDistributions: Plot ms.signal distributions
plotNbIdentificationsVsRT: Plot the number of identified Features per Reteintion Time...
plotNbValidDeFeaturesPerFDR: Plot Total Number of diffrentially Abundant Features...
plotPrecMassErrorDistrib: Plot Precursor Mass Error Distribution
plotPrecMassErrorVsScore: Plot precursorMass error v.s score highlighting decoy and...
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...
plotXYDensity: Scatter plot with density coloring
purityCorrectTMT: Correct channel intensities based on Reporter ion Isotopic...
removeOutliers: Set value to NA if it deviatves with more than 1.5 * IQR from...
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

Functions

COLORS Man page
addIdQvalues Man page Source code
addPTMCoord Source code
addScaffoldPTMFAnnotations Man page Source code
allpValueHist Source code
barplotMSSignal Man page Source code
correlationPlot Source code
createExpDesign Man page Source code
createExpressionDataset Man page Source code
createPairedExpDesign Man page Source code
cvBoxplot Man page Source code
dOverviewPlots Source code
dPlots Source code
dotColorstrip Source code
errorBar Source code
exp2Exprs Source code
expDesignTagToExpDesign Man page Source code
export Man page Source code
filterSQA Source code
getAAProteinCoordinates Man page Source code
getAllCV Man page Source code
getAllEBayes Man page Source code
getBaselineIntensity Man page Source code
getCV Man page Source code
getCalibMixEset Source code
getCalibMixPairedEset Source code
getConditionColors Source code
getControlCondition Source code
getExpDesignProgenesisCsv Man page Source code
getFileType Source code
getFirstEntry Source code
getGlobalNormFactors Man page Source code
getIBAQEset Man page Source code
getIdLevelQvals Man page Source code
getImpuritiesMatrix Man page Source code
getIntSumPerProtein Man page Source code
getLoocvFoldError Man page Source code
getMaxIndex Man page Source code
getMeanCenteredRange Man page Source code
getModifProteinCoordinates Man page Source code
getMotifX Man page Source code
getNbDetectablePeptides Man page Source code
getNbMisCleavages Man page Source code
getNbPeptidesPerProtein Man page Source code
getNbPlex Source code
getNbSpectraPerProtein Man page Source code
getPeptides Man page Source code
getProgenesisCsvExpressionColIndices Source code
getProteaseRegExp Source code
getRTNormFactors Man page Source code
getRatios Man page Source code
getScoreCutOff Man page Source code
getSignalPerCondition Man page Source code
getSkipLineNb Source code
getTopX Man page Source code
getUniquePtmMotifs Source code
getUserOptions Man page Source code
globalNormalize Man page Source code
hClustHeatMap Man page Source code
isCon Man page Source code
isDecoy Man page Source code
isStrippedACs Man page Source code
log2Exprs Source code
maPlotSQ Man page Source code
missinValueBarplot Man page Source code
ntensityAdjustment Source code
option_list Man page
outerLegend Source code
pairsAnnot Man page Source code
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 Source code
plotAdjustedVsNonAdjustedRatio Man page Source code
plotCalibrationCurve Source code
plotExpDesign Man page Source code
plotIdScoreVsFDR Man page Source code
plotMSSignalDistributions Man page Source code
plotNbIdentificationsVsRT Man page Source code
plotNbValidDeFeaturesPerFDR Man page Source code
plotPrecMassErrorDistrib Man page Source code
plotPrecMassErrorVsScore Man page Source code
plotQValueVsPValue Man page Source code
plotROC Man page Source code
plotRTNorm Man page Source code
plotRTNormSummary Man page Source code
plotScoreDistrib Man page Source code
plotVolcano Man page Source code Source code
plotXYDensity Man page Source code
print.safeQuantAnalysis Source code
purityCorrectTMT Man page Source code
qcPlots Source code
removeOutliers Man page Source code
rollUp Man page Source code
rtNormalize Man page Source code
safeQuantAnalysis Man page Source code
setFilter Source code
setNbPeptidesPerProtein Man page Source code
setNbSpectraPerProtein Man page Source code
sqNormalize Man page Source code
standardise Man page Source code
stripACs Man page Source code

Files

inst
inst/manuals
inst/manuals/tsv_spreadsheet_help.pdf
inst/manuals/SafeQuant-man.pdf
inst/manuals/SafeQuant_UseCases.txt
inst/manuals/tsv_spreadsheet_help.docx
exec
exec/installDependencies.R
exec/filterLargeProgenesisPeptideFile.pl
exec/safeQuant.R
exec/roxygenize.R
tests
tests/testSafeQuantAnalysis.R
tests/testData
tests/testData/progenesis_pep_measurement_fractionated1.csv
tests/testData/SQ_Results
tests/testData/SQ_Results/SQ_Results_SQ_PARAMS.TXT
tests/testData/SQ_Results/SQ_Results.pdf
tests/testData/SQ_Results/SQ_Results_PROTEIN.tsv
tests/testData/maxquant_protein_groups.csv
tests/testData/scaffold_tmt10plex_raw_phospho.xls
tests/testData/skyline_transition_results.csv
tests/testData/progenesis_pep_measurement1.csv
tests/testData/scaffold_tmt10plex_calibMix_raw.xls
tests/testData/scaffold_tmt10plex_raw.xls
tests/testData/scaffold_tmt6plex_raw.xls
tests/testData/scaffoldPtm_spectrum_report.xls
tests/testData/progenesis_protein_export1.csv
tests/testData/mouse_proteins.fasta
tests/testData/progenesis_feature_export1.csv
tests/testExpressionAnalysis.R
tests/testUserOptions.R
tests/testParser.R
tests/runAllTest.R
tests/testGraphics.R
tests/testIdentificationAnalysis.R
tests/initTestSession.R
tests/testTMT.R
NAMESPACE
R
R/UserOptions.R
R/SafeQuantAnalysis.R
R/TMT.R
R/Parser.R
R/Graphics.R
R/ExpressionAnalysis.R
R/IdentificationAnalysis.R
README.md
MD5
DESCRIPTION
man
man/getMeanCenteredRange.Rd
man/plotRTNorm.Rd
man/getPeptides.Rd
man/getAllEBayes.Rd
man/plotPrecMassErrorVsScore.Rd
man/getMaxIndex.Rd
man/addScaffoldPTMFAnnotations.Rd
man/plotVolcano.Rd
man/plotXYDensity.Rd
man/plotIdScoreVsFDR.Rd
man/pairsAnnot.Rd
man/cvBoxplot.Rd
man/getIBAQEset.Rd
man/option_list.Rd
man/getScoreCutOff.Rd
man/setNbPeptidesPerProtein.Rd
man/createPairedExpDesign.Rd
man/getRatios.Rd
man/plotPrecMassErrorDistrib.Rd
man/parseProgenesisPeptideMeasurementCsv.Rd
man/getNbDetectablePeptides.Rd
man/perFeatureNormalization.Rd
man/barplotMSSignal.Rd
man/getUserOptions.Rd
man/getLoocvFoldError.Rd
man/addIdQvalues.Rd
man/parseProgenesisProteinCsv.Rd
man/missinValueBarplot.Rd
man/getSignalPerCondition.Rd
man/parseMaxQuantProteinGroupTxt.Rd
man/getBaselineIntensity.Rd
man/getNbSpectraPerProtein.Rd
man/export.Rd
man/isStrippedACs.Rd
man/getExpDesignProgenesisCsv.Rd
man/plotAdjustedVsNonAdjustedRatio.Rd
man/getAAProteinCoordinates.Rd
man/globalNormalize.Rd
man/plotAbsEstCalibrationCurve.Rd
man/maPlotSQ.Rd
man/plotNbValidDeFeaturesPerFDR.Rd
man/setNbSpectraPerProtein.Rd
man/hClustHeatMap.Rd
man/plotROC.Rd
man/plotExpDesign.Rd
man/getModifProteinCoordinates.Rd
man/standardise.Rd
man/isDecoy.Rd
man/getGlobalNormFactors.Rd
man/rollUp.Rd
man/getNbPeptidesPerProtein.Rd
man/getTopX.Rd
man/getRTNormFactors.Rd
man/stripACs.Rd
man/rtNormalize.Rd
man/getMotifX.Rd
man/createExpressionDataset.Rd
man/getAllCV.Rd
man/removeOutliers.Rd
man/getIntSumPerProtein.Rd
man/getCV.Rd
man/createExpDesign.Rd
man/COLORS.Rd
man/isCon.Rd
man/getIdLevelQvals.Rd
man/parseProgenesisFeatureCsv.Rd
man/sqNormalize.Rd
man/plotNbIdentificationsVsRT.Rd
man/plotRTNormSummary.Rd
man/purityCorrectTMT.Rd
man/parseScaffoldPTMReport.Rd
man/getImpuritiesMatrix.Rd
man/plotScoreDistrib.Rd
man/safeQuantAnalysis.Rd
man/plotMSSignalDistributions.Rd
man/plotQValueVsPValue.Rd
man/getNbMisCleavages.Rd
man/parseScaffoldRawFile.Rd
man/expDesignTagToExpDesign.Rd
SafeQuant documentation built on May 19, 2017, 3:48 p.m.