Package index

All functions

Chromatogram() aggregationFun() show(<Chromatogram>) rtime(<Chromatogram>) intensity(<Chromatogram>) mz(<Chromatogram>) precursorMz(<Chromatogram>) fromFile(<Chromatogram>) length(<Chromatogram>) as.data.frame(<Chromatogram>) filterRt(<Chromatogram>) clean(<Chromatogram>) plot(<Chromatogram>,<ANY>) msLevel(<Chromatogram>) isEmpty(<Chromatogram>) productMz(<Chromatogram>) bin(<Chromatogram>) normalize(<Chromatogram>) filterIntensity(<Chromatogram>) alignRt(<Chromatogram>,<Chromatogram>) compareChromatograms(<Chromatogram>,<Chromatogram>) transformIntensity(<Chromatogram>)

Representation of chromatographic MS data

FeatComp-class compfnames-methods compfnames,MSnSet,MSnSet-method compfnames,list,missing-method compfnames show,FeatComp-method names,FeatComp-method common,FeatComp-method common,methods common unique1,FeatComp-method unique1,methods unique1 unique2,FeatComp-method unique2,methods unique2

Class "FeatComp"

FeaturesOfInterest-class FeaturesOfInterest FeaturesOfInterest-methods FeaturesOfInterest,character,character,missing-method FeaturesOfInterest,character,character,MSnSet-method description,FeaturesOfInterest-method foi,FeaturesOfInterest-method foi foi-methods length,FeaturesOfInterest-method show,FeaturesOfInterest-method fnamesIn fnamesIn-methods fnamesIn,FeaturesOfInterest,MSnSet-method fnamesIn,FeaturesOfInterest,matrix-method fnamesIn,FeaturesOfInterest,data.frame-method FoICollection-class FoICollection-methods FoICollection,list-method FoICollection,missing-method FoICollection as.matrix.FoICollection coerce,FoICollection,matrix-method addFeaturesOfInterest addFeaturesOfInterest-methods addFeaturesOfInterest,FeaturesOfInterest,FoICollection-method description,FoICollection-method foi,FoICollection-method length,FoICollection-method lengths,FoICollection-method rmFeaturesOfInterest rmFeaturesOfInterest-methods rmFeaturesOfInterest,FoICollection,numeric-method show,FoICollection-method names,FoICollection-method names<-,FoICollection,character-method [,FoICollection-method [,FoICollection,ANY,ANY-method [,FoICollection,ANY,ANY,ANY-method [[,FoICollection-method [[,FoICollection,ANY,ANY-method

Features of Interest

MChromatograms() show(<MChromatograms>) `[`(<MChromatograms>,<ANY>,<ANY>,<ANY>) `[<-`(<MChromatograms>,<ANY>,<ANY>,<ANY>) plot(<MChromatograms>,<ANY>) phenoData(<MChromatograms>) pData(<MChromatograms>) `pData<-`(<MChromatograms>,<data.frame>) `$`(<MChromatograms>) `$<-`(<MChromatograms>) `colnames<-`(<MChromatograms>,<ANY>) sampleNames(<MChromatograms>) `sampleNames<-`(<MChromatograms>,<ANY>) isEmpty(<MChromatograms>) featureNames(<MChromatograms>) `featureNames<-`(<MChromatograms>) featureData(<MChromatograms>) `featureData<-`(<MChromatograms>,<ANY>) fData(<MChromatograms>) `fData<-`(<MChromatograms>,<ANY>) fvarLabels(<MChromatograms>) `rownames<-`(<MChromatograms>) precursorMz(<MChromatograms>) productMz(<MChromatograms>) mz(<MChromatograms>) polarity(<MChromatograms>) bin(<MChromatograms>) clean(<MChromatograms>) normalize(<MChromatograms>) filterIntensity(<MChromatograms>) alignRt(<MChromatograms>,<Chromatogram>) c(<MChromatograms>) compareChromatograms(<MChromatograms>,<missing>) compareChromatograms(<MChromatograms>,<MChromatograms>) transformIntensity(<MChromatograms>)

Container for multiple Chromatogram objects

MIAPE-class class:MIAPE MIAPE show,MIAPE-method msInfo,MIAPE-method msInfo expemail,MIAPE-method expemail exptitle,MIAPE-method exptitle ionSource,MIAPE-method ionSource ionSourceDetails,MIAPE-method ionSourceDetails analyser,MIAPE-method analyser analyserDetails,MIAPE-method analyserDetails analyzer,MIAPE-method analyzer analyzerDetails,MIAPE-method analyzerDetails detectorType,MIAPE-method detectorType instrumentModel,MIAPE-method instrumentModel instrumentManufacturer,MIAPE-method instrumentManufacturer instrumentCustomisations,MIAPE-method instrumentCustomisations abstract,MIAPE-method samples,MIAPE-method pubMedIds,MIAPE-method pubMedIds<-,MIAPE-method otherInfo,MIAPE-method expinfo,MIAPE-method notes,MIAPE-method notes<-,MIAPE-method combine,MIAPE,MIAPE-method as.MIAME.MIAPE coerce,MIAPE,MIAME-method

The "MIAPE" Class for Storing Proteomics Experiment Information

MSmap-class MSmap MSmap-method MSmap,OnDiskMSnExp-method MSmap,mzRpwiz-method MSmap,mzRramp-method MSmap,mzRraw-method coerce,MSmap,data.frame-method dim,MSmap-method fileName,MSmap-method fileNames,MSmap-method msLevel,MSmap-method msMap,MSmap-method msMap mz,MSmap-method mzRes mzRes,MSmap-method ncol,MSmap-method nrow,MSmap-method plot3D,MSmap-method plot3D plot,MSmap,missing-method rtime,MSmap-method show,MSmap-method t,MSmap-method

Class MSmap

MSnExp-class class:MSnExp MSnExp bin,MSnExp-method clean,MSnExp-method compareSpectra,MSnExp,missing-method extractPrecSpectra,MSnExp-method extractPrecSpectra,MSnExp,numeric-method pickPeaks,MSnExp-method estimateNoise,MSnExp-method plot,MSnExp plot,MSnExp,missing-method quantify,MSnExp-method quantify,OnMSnExp-method quantify,MSnExp,character-method removePeaks,MSnExp-method removeReporters,MSnExp-method removeReporters,OnDiskMSnExp-method smooth,MSnExp-method addIdentificationData,MSnExp,character-method addIdentificationData,MSnExp,mzRident-method addIdentificationData,MSnExp,mzIDClasses-method addIdentificationData,MSnExp,mzID-method addIdentificationData,MSnExp,mzIDCollection-method addIdentificationData,MSnExp,data.frame-method removeNoId,MSnExp-method removeMultipleAssignment,MSnExp-method idSummary,MSnExp-method show,MSnExp-method spectra,MSnExp-method trimMz,MSnExp-method trimMz,MSnExp,numeric-method isolationWindow,MSnExp-method filterMsLevel filterMsLevel,MSnExp-method filterMsLevel,OnDiskMSnExp-method filterPolarity filterPolarity,MSnExp-method filterPolarity,OnDiskMSnExp-method filterMz,MSnExp-method filterMz,OnDiskMSnExp-method filterRt filterRt,MSnExp-method filterRt,OnDiskMSnExp-method filterFile filterFile,MSnExp-method filterFile,OnDiskMSnExp-method filterAcquisitionNum filterAcquisitionNum,MSnExp-method filterAcquisitionNum,OnDiskMSnExp-method filterEmptySpectra filterEmptySpectra,MSnExp-method filterEmptySpectra,OnDiskMSnExp-method filterPrecursorScan filterPrecursorScan,MSnExp-method filterPrecursorScan,OnDiskMSnExp-method filterPrecursorMz filterPrecursorMz,MSnExp-method filterIsolationWindow filterIsolationWindow,MSnExp-method isCentroided,MSnExp-method all.equal,MSnExp,MSnExp-method all.equal,MSnExp,OnDiskMSnExp-method all.equal,OnDiskMSnExp,MSnExp-method all.equal,OnDiskMSnExp,OnDiskMSnExp-method splitByFile splitByFile,MSnExp,factor-method splitByFile,OnDiskMSnExp,factor-method coerce,MSnExp,data.frame-method as.data.frame.MSnExp coerce,MSnExp,MSpectra-method

The 'MSnExp' Class for MS Data And Meta-Data

MSnProcess-class class:MSnProcess MSnProcess fileNames,MSnProcess-method show,MSnProcess-method combine,MSnProcess,MSnProcess-method coerce,MSnProcess,list-method

The "MSnProcess" Class

MSnSet-class class:MSnSet MSnSet acquisitionNum,MSnSet-method exprs,MSnSet-method dim,MSnSet-method fileNames,MSnSet-method msInfo,MSnSet-method processingData,MSnSet-method qual,MSnSet-method qual show,MSnSet-method purityCorrect,MSnSet-method purityCorrect,MSnSet,matrix-method meanSdPlot,MSnSet-method t.MSnSet [,MSnSet-method [,MSnSet,ANY,ANY-method [,MSnSet,ANY,ANY,ANY-method as.ExpressionSet.MSnSet as.MSnSet.ExpressionSet as.data.frame.MSnSet ms2df coerce,IBSpectra,MSnSet-method coerce,MSnSet,ExpressionSet-method coerce,ExpressionSet,MSnSet-method coerce,MSnSet,data.frame-method coerce,MSnSet,SummarizedExperiment-method coerce,SummarizedExperiment,MSnSet-method addMSnSetMetadata write.exprs write.exprs,MSnSet-method experimentData<-,MSnSet,MIAPE-method pData<-,MSnSet,data.frame-method fData<-,MSnSet,data.frame-method combine,MSnSet,MSnSet-method topN,MSnSet,MSnSet-method topN,MSnSet-method topN,matrix-method topN filterNA,MSnSet-method filterNA,matrix-method filterNA filterZero,MSnSet-method filterZero,matrix-method filterZero filterMsLevel,MSnSet-method log,MSnSet-method image,MSnSet-method image2 MAplot,MSnSet-method addIdentificationData,MSnSet,character-method addIdentificationData,MSnSet,mzIDClasses-method addIdentificationData,MSnSet,mzID-method addIdentificationData,MSnSet,mzRident-method addIdentificationData,MSnSet,mzIDCollection-method addIdentificationData,MSnSet,data.frame-method removeNoId,MSnSet-method removeMultipleAssignment-method removeMultipleAssignment,MSnSet-method removeMultipleAssignment idSummary,MSnSet-method idSummary fromFile,MSnSet-method trimws trimws,MSnSet-method trimws,data.frame-method exptitle,MSnSet-method expemail,MSnSet-method ionSource,MSnSet-method analyser,MSnSet-method analyzer,MSnSet-method detectorType,MSnSet-method description,MSnSet-method updateFvarLabels updateSampleNames updateFeatureNames droplevels.MSnSet

The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data

MSnSetList-class MSnSetList msnsets objlog [,MSnSetList,ANY,ANY,ANY-method [,MSnSetList,ANY,missing,missing-method [[,MSnSetList,ANY,ANY-method [[,MSnSetList,ANY,missing-method length,MSnSetList-method show,MSnSetList-method names,MSnSetList-method names<-,MSnSetList,ANY-method split,MSnSet,factor-method split,MSnSet,character-method unsplit,MSnSetList,factor-method lapply,MSnSetList-method sapply,MSnSetList-method fData,MSnSetList-method fData<-,MSnSetList,DataFrame-method

Storing multiple related MSnSets

MSnbaseOptions() isMSnbaseVerbose() setMSnbaseVerbose() setMSnbaseParallelThresh() setMSnbaseFastLoad() isMSnbaseFastLoad()

MSnbase options

MSpectra() mz(<MSpectra>) intensity(<MSpectra>) rtime(<MSpectra>) precursorMz(<MSpectra>) precursorCharge(<MSpectra>) precScanNum(<MSpectra>) precursorIntensity(<MSpectra>) acquisitionNum(<MSpectra>) scanIndex(<MSpectra>) peaksCount(<MSpectra>,<ANY>) msLevel(<MSpectra>) tic(<MSpectra>) ionCount(<MSpectra>) collisionEnergy(<MSpectra>) fromFile(<MSpectra>) polarity(<MSpectra>) smoothed(<MSpectra>) isEmpty(<MSpectra>) centroided(<MSpectra>) isCentroided(<MSpectra>) writeMgfData(<MSpectra>) clean(<MSpectra>) removePeaks(<MSpectra>) filterMz(<MSpectra>) pickPeaks(<MSpectra>) smooth(<MSpectra>) filterMsLevel(<MSpectra>)

List of Spectrum objects along with annotations

MzTab-class class:MzTab MzTab metadata,MzTab-method fileName,MzTab-method fileNames,MzTab-method peptides,MzTab-method proteins,MzTab-method psms,MzTab-method comments smallMolecules moleculeFeatures moleculeEvidence mzTabMode mzTabType coerce,MzTab,MSnSetList-method show,MzTab-method

Parse MzTab files

OnDiskMSnExp-class class:OnDiskMSnExp OnDiskMSnExp show,OnDiskMSnExp-method [,OnDiskMSnExp,ANY,ANY,ANY-method [,OnDiskMSnExp,logicalOrNumeric,missing,missing-method [[,OnDiskMSnExp-method [[,OnDiskMSnExp,ANY,ANY-method [[,OnDiskMSnExp,ANY,ANY,missing-method [[,OnDiskMSnExp,ANY,missing,missing-method acquisitionNum,OnDiskMSnExp-method assayData,OnDiskMSnExp-method isCentroided,OnDiskMSnExp-method centroided,OnDiskMSnExp-method centroided<-,OnDiskMSnExp,logical-method smoothed,OnDiskMSnExp-method smoothed<-,OnDiskMSnExp,logical-method fromFile,OnDiskMSnExp-method header,OnDiskMSnExp,missing-method header,OnDiskMSnExp,numeric-method ionCount,OnDiskMSnExp-method intensity,OnDiskMSnExp-method length,OnDiskMSnExp-method msLevel,OnDiskMSnExp-method mz,OnDiskMSnExp-method peaksCount,OnDiskMSnExp,missing-method peaksCount,OnDiskMSnExp,numeric-method polarity,OnDiskMSnExp-method rtime,OnDiskMSnExp-method scanIndex,OnDiskMSnExp-method spectra,OnDiskMSnExp-method tic,OnDiskMSnExp-method bpi,OnDiskMSnExp-method bpi precScanNum,OnDiskMSnExp-method featureNames<-,OnDiskMSnExp-method featureNames<-,OnDiskMSnExp,ANY-method featureNames,OnDiskMSnExp-method precScanNum,OnDiskMSnExp-method precursorIntensity,OnDiskMSnExp-method collisionEnergy,OnDiskMSnExp-method isolationWindowLowerMz,OnDiskMSnExp-method isolationWindowUpperMz,OnDiskMSnExp-method compareSpectra,OnDiskMSnExp,missing-method estimateNoise,OnDiskMSnExp-method extractPrecSpectra,OnDiskMSnExp,numeric-method pickPeaks,OnDiskMSnExp-method precursorCharge,OnDiskMSnExp-method precursorMz,OnDiskMSnExp-method quantify,OnDiskMSnExp-method smooth,OnDiskMSnExp-method spectrapply,OnDiskMSnExp-method clean,OnDiskMSnExp-method removePeaks,OnDiskMSnExp-method bin,OnDiskMSnExp-method trimMz,OnDiskMSnExp,numeric-method normalize,OnDiskMSnExp-method normalise,OnDiskMSnExp-method validateOnDiskMSnExp coerce,OnDiskMSnExp,MSnExp-method as.MSnExp.OnDiskMSnExp

The OnDiskMSnExp Class for MS Data And Meta-Data

ProcessingStep-class ProcessingStep:OnDiskMSnExp ProcessingStep show,ProcessingStep-method executeProcessingStep

Simple processing step class

ReporterIons-class class:ReporterIons ReporterIons show,ReporterIons-method [,ReporterIons-method [,ReporterIons,ANY,ANY-method [,ReporterIons,ANY,ANY,ANY-method length-method length,ReporterIons-method mz,ReporterIons-method reporterColours-method reporterColours,ReporterIons-method reporterColours reporterColors-method reporterColors,ReporterIons-method reporterColors reporterNames-method reporterNames,ReporterIons-method reporterNames reporterNames<-,ReporterIons-method reporterNames<-,ReporterIons,ANY-method reporterNames<-,ReporterIons,character-method reporterNames<- width-method width,ReporterIons-method width names,ReporterIons-method description,ReporterIons-method

The "ReporterIons" Class

Spectrum-class class:Spectrum Spectrum acquisitionNum,Spectrum-method acquisitionNum scanIndex,Spectrum-method scanIndex fromFile,Spectrum-method fromFile intensity,Spectrum-method intensity msLevel,Spectrum-method msLevel mz,Spectrum-method mz peaksCount,Spectrum,missing-method peaksCount rtime,Spectrum-method rtime tic,Spectrum-method tic ionCount,Spectrum-method ionCount isCentroided,Spectrum-method isCentroided centroided,Spectrum-method centroided centroided<-,Spectrum,ANY-method centroided<-,Spectrum,logical-method centroided<- polarity,Spectrum-method polarity smoothed,Spectrum-method smoothed smoothed<-,Spectrum,ANY-method smoothed<-,Spectrum,logical-method smoothed<- bin,Spectrum-method clean,Spectrum-method compareSpectra,Spectrum,Spectrum-method estimateNoise,Spectrum-method pickPeaks,Spectrum-method quantify,Spectrum-method quantify,Spectrum,character-method removePeaks,Spectrum-method show,Spectrum-method smooth,Spectrum-method trimMz,Spectrum-method trimMz,Spectrum,numeric-method filterMz,Spectrum-method filtermz,Spectrum,numeric-method isEmpty,Spectrum-method isEmpty,environment-method coerce,Spectrum,data.frame-method as.data.frame.Spectrum

The "Spectrum" Class

Spectrum1-class class:Spectrum1 Spectrum1

The "Spectrum1" Class for MS1 Spectra

Spectrum2-class class:Spectrum2 Spectrum2 precursorMz,Spectrum-method precursorMz precScanNum,Spectrum-method precScanNum precAcquisitionNum,Spectrum-method precAcquisitionNum precursorIntensity,Spectrum-method precursorIntensity precursorCharge,Spectrum-method precursorCharge collisionEnergy,Spectrum-method collisionEnergy removeReporters,Spectrum-method calculateFragments,character,Spectrum2-method

The "Spectrum2" Class for MSn Spectra

TMT6 TMT6b TMT7 TMT7b TMT10 TMT10ETD TMT10HCD TMT11 TMT11HCD

TMT 6/10-plex sets

addIdentificationData-methods addIdentificationData

Adds Identification Data

aggvar()

Identify aggregation outliers

averageMSnSet()

Generate an average MSnSet

bin-methods bin

Bin 'MSnExp' or 'Spectrum' instances

calculateFragments calculateFragments,character,missing-method

Calculate ions produced by fragmentation.

chromatogram(<MSnExp>)

Extract chromatogram object(s)

clean-methods clean

Clean 'MSnExp', 'Spectrum' or 'Chromatogram' instances

combineFeatures combineFeatures,MSnSet-method

Combines features in an MSnSet object

combineSpectra(<MSnExp>) combineSpectra(<MSpectra>)

Combine Spectra

combineSpectraMovingWindow()

Combine signal from consecutive spectra of LCMS experiments

commonFeatureNames()

Keep only common feature names

compareMSnSets()

Compare two MSnSets

compareSpectra-methods compareSpectra

Compare Spectra of an 'MSnExp' or 'Spectrum' instances

consensusSpectrum()

Combine spectra to a consensus spectrum

estimateMzResolution(<MSnExp>) estimateMzResolution(<Spectrum>)

Estimate the m/z resolution of a spectrum

estimateMzScattering()

Estimate m/z scattering in consecutive scans

estimateNoise-methods estimateNoise

Noise Estimation for 'Spectrum' instances

extractPrecSpectra-methods extractPrecSpectra

Extracts precursor-specific spectra from an 'MSnExp' object

extractSpectraData()

Conversion between objects from the Spectra and MSnbase packages

expandFeatureVars() mergeFeatureVars()

Expand or merge feature variables

factorsAsStrings()

Converts factors to strings

featureCV()

Calculates coeffivient of variation for features

fillUp()

Fills up a vector

filterIdentificationDataFrame()

Filter out unreliable PSMs.

formatRt()

Format Retention Time

getVariableName()

Return a variable name

grepEcols() getEcols()

Returns the matching column names of indices.

hasSpectra() hasChromatograms()

Checks if raw data files have any spectra or chromatograms

iPQF()

iPQF: iTRAQ (and TMT) Protein Quantification based on Features

iTRAQ4 iTRAQ5 iTRAQ8 iTRAQ9

iTRAQ 4-plex set

imageNA2()

NA heatmap visualisation for 2 groups

impute(<MSnSet>)

Quantitative proteomics data imputation

isCentroidedFromFile()

Get mode from mzML data file

itraqdata

Example MSnExp and MSnSet data sets

listOf()

Tests equality of list elements class

makeCamelCase()

Convert to camel case by replacing dots by captial letters

makeNaData() makeNaData2() whichNA()

Create a data with missing values

meanMzInts()

Combine a list of spectra to a single spectrum

missing-data missingdata

Documenting missing data visualisation

as as.data.frame.mzRident

Coerce identification data to a data.frame

nFeatures()

How many features in a group?

nQuants()

Count the number of quantitfied features.

naplot()

Overview of missing value

normToReference()

Combine peptides into proteins.

normalise-methods normalise,Spectrum-method normalise,Spectrum2-method normalise,MSnSet-method normalise,MSnExp-method normalize-methods normalize,Spectrum-method normalize,Spectrum2-method normalize,MSnSet-method normalize,MSnExp-method scale,MSnSet-method normalise normalize

Normalisation of MSnExp, MSnSet and Spectrum objects

npcv()

Non-parametric coefficient of variation

pSet-class pSet class:pSet [,pSet-method [,pSet,ANY,ANY-method [,pSet,ANY,ANY,ANY-method [[,pSet-method [[,pSet,ANY,ANY-method $,pSet-method $<-,pSet-method abstract,pSet-method acquisitionNum,pSet-method scanIndex,pSet-method assayData,pSet-method collisionEnergy,pSet-method dim,pSet-method dim experimentData,pSet-method fData,pSet-method fData<-,pSet,data.frame-method featureData,pSet-method featureNames,pSet-method fileNames,pSet-method fileNames fromFile,pSet-method centroided,pSet-method centroided<-,pSet,ANY-method centroided<-,pSet,logical-method smoothed,pSet-method smoothed<-,pSet,ANY-method smoothed<-,pSet,logical-method fvarLabels,pSet-method fvarMetadata,pSet-method header,pSet,missing-method header,pSet,numeric-method header intensity,pSet-method length,pSet-method length msInfo,pSet-method msLevel,pSet-method mz,pSet-method notes,pSet-method pData,pSet-method pData<-,pSet,ANY-method peaksCount,pSet,missing-method peaksCount,pSet,numeric-method phenoData,pSet-method phenoData<-,pSet,ANY-method polarity,pSet-method precursorCharge,pSet-method precursorIntensity,pSet-method precursorMz,pSet-method precScanNum,pSet-method precAcquisitionNum,pSet-method processingData,pSet-method processingData protocolData,pSet-method pubMedIds,pSet-method rtime,pSet-method sampleNames,pSet-method sampleNames<-,pSet,character-method spectra,pSet-method spectra tic,pSet-method ionCount,pSet-method varLabels,pSet-method varMetadata,pSet-method exptitle,pSet-method expemail,pSet-method ionSource,pSet-method ionSourceDetails,pSet-method analyser,pSet-method analyzer,pSet-method analyserDetails,pSet-method analyzerDetails,pSet-method instrumentModel,pSet-method instrumentManufacturer,pSet-method instrumentCustomisations,pSet-method detectorType,pSet-method description,pSet-method isolationWindowLowerMz isolationWindowUpperMz isolationWindowLowerMz,pSet-method isolationWindowUpperMz,pSet-method spectrapply spectrapply,pSet-method coerce,AnnotatedDataFrame,list-method coerce,MIAxE,list-method

Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata

pickPeaks-methods pickPeaks

Peak Detection for 'MSnExp' or 'Spectrum' instances

plot,Spectrum-method plot,Spectrum,missing-method plot,Spectrum2,character-method plot-methods plot.MSnExp plot.Spectrum plot.Spectrum.character plot

Plotting 'MSnExp' and 'Spectrum' object(s)

plot2d-methods plot2d,MSnExp-method plot2d,data.frame-method plot2d

The 'plot2d' method for 'MSnExp' quality assessment

plotDensity-methods plotDensity,MSnExp-method plotDensity,data.frame-method plotDensity

The 'plotDensity' method for 'MSnExp' quality assessment

plotMzDelta-methods plotMzDelta,MSnExp-method plotMzDelta,mzRramp-method plotMzDelta

The delta m/z plot

plotNA-methods plotNA,MSnSet-method plotNA,matrix-method plotNA is.na.MSnSet

Exploring missing data in 'MSnSet' instances

plot.Spectrum.Spectrum plot,Spectrum,Spectrum-method

Plotting a 'Spectrum' vs another 'Spectrum' object.

precSelection()

Number of precursor selection events

purityCorrect-methods purityCorrect makeImpuritiesMatrix

Performs reporter ions purity correction

quantify-methods quantify

Quantifies 'MSnExp' and 'Spectrum' objects

readMSData()

Imports mass-spectrometry raw data files as 'MSnExp' instances.

readMSnSet() readMSnSet2()

Read 'MSnSet'

readMgfData()

Import mgf files as 'MSnExp' instances.

readMzIdData()

Import peptide-spectrum matches

readMzTabData()

Read an 'mzTab' file

readMzTabData_v0.9()

Read an 'mzTab' file

readSRMData()

Read SRM/MRM chromatographic data

reduce(<data.frame>)

Reduce a data.frame

removeNoId-methods removeNoId

Removes non-identified features

removePeaks-methods removePeaks

Removes low intensity peaks

removeReporters-methods removeReporters

Removes reporter ion tag peaks

selectFeatureData() requiredFvarLabels()

Select feature variables of interest

smooth-methods smooth

Smooths 'MSnExp' or 'Spectrum' instances

trimMz-methods trimMz filterMz filterMz-methods

Trims 'MSnExp' or 'Spectrum' instances

updateObject,MSnExp-method updateObject,Spectrum-method

Update MSnbase objects

writeMSData(<MSnExp>,<character>)

Write MS data to mzML or mzXML files

writeMgfData writeMgfData-methods writeMgfData,MSnExp-method writeMgfData,Spectrum-method

Write an experiment or spectrum to an mgf file

writeMzTabData()

Export an MzTab object as mzTab file.