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.

Author
Erik Ahrne
Date of publication
2016-10-04 16:47:59
Maintainer
Erik Ahrne <erik.ahrne@unibas.ch>
License
GPL-3
Version
2.3

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
calibrationCurve
S3 class object describing a calibration curve and storing...
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/skyline_dilution_curve.csv
SafeQuant/tests/testData/maxquant_protein_groups.csv
SafeQuant/tests/testData/scaffold_tmt10plex_raw_phospho.xls
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/testTargeted.R
SafeQuant/tests/testTMT.R
SafeQuant/NAMESPACE
SafeQuant/R
SafeQuant/R/Targeted.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/calibrationCurve.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