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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

Install

install.packages('SafeQuant')

Monthly Downloads

Version

2.2.1

License

GPL-3

Maintainer

Erik Ahrne

Last Published

January 6th, 2016

Functions in SafeQuant (2.2.1)

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

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)