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>)
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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
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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-method [,FoICollection,ANY,ANY-method [,FoICollection,ANY,ANY,ANY-method [[,FoICollection-method [[,FoICollection,ANY,ANY-method
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Features of Interest |
MChromatograms() show(<MChromatograms>) `[`(<MChromatograms>,<ANY>,<ANY>,<ANY>) `[<-`(<MChromatograms>) plot(<MChromatograms>,<ANY>) phenoData(<MChromatograms>) pData(<MChromatograms>) `pData<-`(<MChromatograms>,<data.frame>) `$`(<MChromatograms>) `$<-`(<MChromatograms>) `colnames<-`(<MChromatograms>) 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>)
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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 otherInfo,MIAPE-method expinfo,MIAPE-method notes,MIAPE-method notes combine,MIAPE,MIAPE-method as.MIAME.MIAPE coerce,MIAPE,MIAME-method
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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
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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
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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
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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 pData fData 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
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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 split,MSnSet,factor-method split,MSnSet,character-method unsplit,MSnSetList,factor-method lapply,MSnSetList-method sapply,MSnSetList-method fData,MSnSetList-method fData
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Storing multiple related MSnSets |
MSnbaseOptions() isMSnbaseVerbose() setMSnbaseVerbose() setMSnbaseParallelThresh() setMSnbaseFastLoad() isMSnbaseFastLoad()
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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>)
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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
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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 smoothed,OnDiskMSnExp-method smoothed 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 featureNames 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
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The OnDiskMSnExp Class for MS Data And Meta-Data |
ProcessingStep-class ProcessingStep:OnDiskMSnExp ProcessingStep show,ProcessingStep-method executeProcessingStep
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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 reporterNames reporterNames reporterNames width-method width,ReporterIons-method width names,ReporterIons-method description,ReporterIons-method
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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 centroided centroided polarity,Spectrum-method polarity smoothed,Spectrum-method smoothed smoothed smoothed 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
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The "Spectrum" Class |
Spectrum1-class class:Spectrum1 Spectrum1
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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
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The "Spectrum2" Class for MSn Spectra |
TMT6 TMT6b TMT7 TMT7b TMT10 TMT10ETD TMT10HCD TMT11 TMT11HCD
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TMT 6/10-plex sets |
addIdentificationData-methods addIdentificationData
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Adds Identification Data |
aggvar()
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Identify aggregation outliers |
averageMSnSet()
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Generate an average MSnSet |
bin-methods bin
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Bin 'MSnExp' or 'Spectrum' instances |
calculateFragments calculateFragments,character,missing-method
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Calculate ions produced by fragmentation. |
chromatogram(<MSnExp>)
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Extract chromatogram object(s) |
clean-methods clean
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Clean 'MSnExp', 'Spectrum' or 'Chromatogram' instances |
combineFeatures combineFeatures,MSnSet-method
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Combines features in an MSnSet object |
combineSpectra(<MSnExp>) combineSpectra(<MSpectra>)
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Combine Spectra |
combineSpectraMovingWindow()
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Combine signal from consecutive spectra of LCMS experiments |
commonFeatureNames()
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Keep only common feature names |
compareMSnSets()
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Compare two MSnSets |
compareSpectra-methods compareSpectra
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Compare Spectra of an 'MSnExp' or 'Spectrum' instances |
consensusSpectrum()
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Combine spectra to a consensus spectrum |
estimateMzResolution(<MSnExp>) estimateMzResolution(<Spectrum>)
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Estimate the m/z resolution of a spectrum |
estimateMzScattering()
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Estimate m/z scattering in consecutive scans |
estimateNoise-methods estimateNoise
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Noise Estimation for 'Spectrum' instances |
extractPrecSpectra-methods extractPrecSpectra
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Extracts precursor-specific spectra from an 'MSnExp' object |
extractSpectraData()
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Extract data from MSnbase objects for use in Spectra |
expandFeatureVars() mergeFeatureVars()
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Expand or merge feature variables |
factorsAsStrings()
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Converts factors to strings |
featureCV()
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Calculates coeffivient of variation for features |
fillUp()
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Fills up a vector |
filterIdentificationDataFrame()
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Filter out unreliable PSMs. |
formatRt()
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Format Retention Time |
getVariableName()
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Return a variable name |
grepEcols() getEcols()
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Returns the matching column names of indices. |
hasSpectra() hasChromatograms()
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Checks if raw data files have any spectra or chromatograms |
iPQF()
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iPQF: iTRAQ (and TMT) Protein Quantification based on Features |
iTRAQ4 iTRAQ5 iTRAQ8 iTRAQ9
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iTRAQ 4-plex set |
imageNA2()
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NA heatmap visualisation for 2 groups |
impute(<MSnSet>)
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Quantitative proteomics data imputation |
isCentroidedFromFile()
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Get mode from mzML data file |
itraqdata
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Example MSnExp and MSnSet data sets |
listOf()
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Tests equality of list elements class |
makeCamelCase()
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Convert to camel case by replacing dots by captial letters |
makeNaData() makeNaData2() whichNA()
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Create a data with missing values |
meanMzInts()
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Combine a list of spectra to a single spectrum |
missing-data missingdata
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Documenting missing data visualisation |
as as.data.frame.mzRident
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Coerce identification data to a data.frame |
nFeatures()
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How many features in a group? |
nQuants()
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Count the number of quantitfied features. |
naplot()
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Overview of missing value |
navMS() nextMS() prevMS()
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Navigate an MSnExp object |
normToReference()
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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
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Normalisation of MSnExp , MSnSet and Spectrum objects |
npcv()
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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 $ 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 featureData,pSet-method featureNames,pSet-method fileNames,pSet-method fileNames fromFile,pSet-method centroided,pSet-method centroided centroided smoothed,pSet-method smoothed smoothed 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 peaksCount,pSet,missing-method peaksCount,pSet,numeric-method phenoData,pSet-method phenoData 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 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
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Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
pickPeaks-methods pickPeaks
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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
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Plotting 'MSnExp' and 'Spectrum' object(s) |
plot2d-methods plot2d,MSnExp-method plot2d,data.frame-method plot2d
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The 'plot2d' method for 'MSnExp' quality assessment |
plotDensity-methods plotDensity,MSnExp-method plotDensity,data.frame-method plotDensity
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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
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Exploring missing data in 'MSnSet' instances |
plot.Spectrum.Spectrum plot,Spectrum,Spectrum-method
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Plotting a 'Spectrum' vs another 'Spectrum' object. |
precSelection()
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Number of precursor selection events |
purityCorrect-methods purityCorrect makeImpuritiesMatrix
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Performs reporter ions purity correction |
quantify-methods quantify
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Quantifies 'MSnExp' and 'Spectrum' objects |
readMSData()
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Imports mass-spectrometry raw data files as 'MSnExp' instances. |
readMSnSet() readMSnSet2()
|
Read 'MSnSet' |
readMgfData()
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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
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Removes reporter ion tag peaks |
selectFeatureData() requiredFvarLabels()
|
Select feature variables of interest |
smooth-methods smooth
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Smooths 'MSnExp' or 'Spectrum' instances |
trimMz-methods trimMz filterMz filterMz-methods
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Trims 'MSnExp' or 'Spectrum' instances |
updateObject,MSnExp-method updateObject,Spectrum-method
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Update MSnbase objects |
writeMSData(<MSnExp>,<character>)
|
Write MS data to mzML or mzXML files |
writeMgfData writeMgfData-methods writeMgfData,MSnExp-method writeMgfData,Spectrum-method
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Write an experiment or spectrum to an mgf file |
writeMzTabData()
|
Export an MzTab object as mzTab file. |