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SafeQuant (version 2.2.1)
A Toolbox for the Analysis of Proteomics Data
Description
Tools for the statistical analysis and visualization of (relative and absolute) quantitative (LFQ,TMT,HRM) Proteomics data.
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Version
2.3.1
2.3
2.2.2
2.2.1
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Install
install.packages('SafeQuant')
Monthly Downloads
40
Version
2.2.1
License
GPL-3
Maintainer
Erik Ahrne
Last Published
January 6th, 2016
Functions in SafeQuant (2.2.1)
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calibrationCurve
S3 class object describing a calibration curve and storing some figures of merit
getLoocvFoldError
Leave-One-Out Cross Validate Qunatification Model
getRatios
Calculate ratios, comparing all case to control
addIdQvalues
Add identification leve q-values to ExpressionSet (calculated based on target-decoy score distribution)
COLORS
color vector
getNbSpectraPerProtein
Get number of spectra per protein
getBaselineIntensity
Get signal at zscore x (x standard deviations below mean)
expDesignTagToExpDesign
Create experimental design data.frame from user input string
getMotifX
Create motif-x peptide annotation
getPeptides
Digest protein
createExpressionDataset
Create ExpressionSet object
pairsAnnot
Plot lower triangle Pearsons R^2. Diagonal text, upper triangle all against all scatter plots with lm abline
getMaxIndex
get index of max in vecotr of numeric values
missinValueBarplot
Plot Percentage of Features with with missing values
getSignalPerCondition
Summarize replicate signal per condition (min)
getTopX
Calculate Mean of X most intense features
getGlobalNormFactors
Get normalization factors. calculated as summed/median signal per run (column) over summed/median of first run.
getRTNormFactors
Get retentiontime base normalization factors
addScaffoldPTMFAnnotations
Add scaffold ptm annotaitons to tmt experiment
hClustHeatMap
Hierarchical clustering heat map, cluster by runs intensity, features by ratio and display log2 ratios to control median
createExpDesign
Create Experimental Design
plotRTNormSummary
Plot all retention time normalization profiles
plotIdScoreVsFDR
Plot FDR vs. identification score
getNbDetectablePeptides
Get number peptides passing defined length criteria
getIntSumPerProtein
Sum up raw intensities per protein and channel. keep track of number of summed spectra and unique peptides
plotAbsEstCalibrationCurve
Plot absolut Estimation calibration Curve
plotVolcano
Plots volcano, data points colored by max cv of the 2 compared conditions
globalNormalize
Normalize, Norm factors calculated as median signal per run (column) over median of first run.
getAAProteinCoordinates
Get amino acid coordinates on protein
getMeanCenteredRange
Get modification coordinates on protein
getNbPeptidesPerProtein
Get number of peptides per protein
getScoreCutOff
Get score cutoff for a given fdr cut-off
getIdLevelQvals
Calculates identification level q-values based on target-decoy score distributions
isDecoy
Check if protein is a decoy entry
plotExpDesign
Display experimental design, high-lighting the control condition
rollUp
Roll up feature intensites per unique colum combination
parseProgenesisPeptideMeasurementCsv
Parse Progenesis Peptide Measurement Csv Export
parseProgenesisProteinCsv
Parse Progenesis Protein Csv
isCon
Check if protein is a contaminant entry
getAllEBayes
Perform statistical test (mderated t-test), comparing all case to control
plotScoreDistrib
Plot identifications target decoy distribution
getCV
Calculate Coefficiant of Variance per feature (Relative standard Deviation)
getAllCV
Calculate Coefficiant of Variance per feature (Relative standard Deviation) per Condition
getImpuritiesMatrix
Get Thermo TMT impurity matrix
barplotMSSignal
Barplot of ms-signal per column
getExpDesignProgenesisCsv
Parse Experimental Design from Progenesis Csv Export
getIBAQEset
Calculate intensity-based absolute-protein-quantification (iBAQ) metric per protein
plotMSSignalDistributions
Plot ms.signal distributions
stripACs
strip uniprot format e.g. "sp|Q8CHJ2|AQP12_MOUSE" -> Q8CHJ2
parseMaxQuantProteinGroupTxt
Parse MaxQuant Protein Group Txt
setNbSpectraPerProtein
Set nbPeptides coulmn of featureData
standardise
Standardise data
export
Export content of safeQuantAnalysis object
plotRTNorm
Plot all retention time profile overalying ratios
plotNbValidDeFeaturesPerFDR
Plot Total Number of diffrentially Abundant Features (applying ratio cutoff) vs. qValue/pValue for all conditions
plotXYDensity
Scatter plot with density coloring
setNbPeptidesPerProtein
Set nbPeptides coulmn of featureData
purityCorrectTMT
Correct channel intensities based on Reporter ion Isotopic Distributions
perFeatureNormalization
Per Feature Normalization
plotQValueVsPValue
Plot qValue vs pValue
plotROC
Plot Number of Identifications vs. FDR
plotNbIdentificationsVsRT
Plot the number of identified Features per Reteintion Time minute.
rtNormalize
Normalization data per retention time bin
getUserOptions
Read User Specified Command Line Options
isStrippedACs
Check if ACs are in "non-stripped" uniprot format e.g. "sp|Q8CHJ2|AQP12_MOUSE"
plotPrecMassErrorVsScore
Plot precursorMass error v.s score highlighting decoy and displaying user specified user specified precursor mass filter
plotPrecMassErrorDistrib
Plot Precursor Mass Error Distribution
getModifProteinCoordinates
Get modification coordinates on protein
parseProgenesisFeatureCsv
Parse Progenesis Feature Csv Export
option_list
Command Line Option List
removeOutliers
Set value to NA if it deviatves with more than 1.5 * IQR from lower/upper quantile
sqNormalize
Normalize
cvBoxplot
C.V. boxplot
getNbMisCleavages
Get number of mis-cleavages perp peptide
safeQuantAnalysis
safeQunat s3 class
parseScaffoldPTMReport
Parse scaffold PTM Spectrum Report
parseScaffoldRawFile
Parse scaffold output .xls file (RAW export)