SafeQuant: A Toolbox for the Analysis of Proteomics Data

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

AuthorErik Ahrne
Date of publication2016-12-06 14:04:35
MaintainerErik Ahrne <erik.ahrne@unibas.ch>
LicenseGPL-3
Version2.3.1

View on CRAN

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

Files in this package

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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