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

Functions

addIdQvalues Man page
addScaffoldPTMFAnnotations Man page
barplotMSSignal Man page
COLORS Man page
createExpDesign Man page
createExpressionDataset Man page
createPairedExpDesign Man page
cvBoxplot Man page
expDesignTagToExpDesign Man page
export Man page
getAAProteinCoordinates Man page
getAllCV Man page
getAllEBayes Man page
getBaselineIntensity Man page
getCV Man page
getExpDesignProgenesisCsv Man page
getGlobalNormFactors Man page
getIBAQEset Man page
getIdLevelQvals Man page
getImpuritiesMatrix Man page
getIntSumPerProtein Man page
getLoocvFoldError Man page
getMaxIndex Man page
getMeanCenteredRange Man page
getModifProteinCoordinates Man page
getMotifX Man page
getNbDetectablePeptides Man page
getNbMisCleavages Man page
getNbPeptidesPerProtein Man page
getNbSpectraPerProtein Man page
getPeptides Man page
getRatios Man page
getRTNormFactors Man page
getScoreCutOff Man page
getSignalPerCondition Man page
getTopX Man page
getUserOptions Man page
globalNormalize Man page
hClustHeatMap Man page
isCon Man page
isDecoy Man page
isStrippedACs Man page
maPlotSQ Man page
missinValueBarplot Man page
option_list Man page
pairsAnnot Man page
parseMaxQuantProteinGroupTxt Man page
parseProgenesisFeatureCsv Man page
parseProgenesisPeptideMeasurementCsv Man page
parseProgenesisProteinCsv Man page
parseScaffoldPTMReport Man page
parseScaffoldRawFile Man page
perFeatureNormalization Man page
plotAbsEstCalibrationCurve Man page
plotAdjustedVsNonAdjustedRatio Man page
plotExpDesign Man page
plotIdScoreVsFDR Man page
plotMSSignalDistributions Man page
plotNbIdentificationsVsRT Man page
plotNbValidDeFeaturesPerFDR Man page
plotPrecMassErrorDistrib Man page
plotPrecMassErrorVsScore Man page
plotQValueVsPValue Man page
plotROC Man page
plotRTNorm Man page
plotRTNormSummary Man page
plotScoreDistrib Man page
plotVolcano Man page
plotXYDensity Man page
purityCorrectTMT Man page
removeOutliers Man page
rollUp Man page
rtNormalize Man page
safeQuantAnalysis Man page
setNbPeptidesPerProtein Man page
setNbSpectraPerProtein Man page
sqNormalize Man page
standardise Man page
stripACs Man page

Files

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.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.