Package: MSnbase 2.31.1
Laurent Gatto
MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics
MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
Authors:
MSnbase_2.31.1.tar.gz
MSnbase_2.31.1.zip(r-4.5)MSnbase_2.31.1.zip(r-4.4)MSnbase_2.31.1.zip(r-4.3)
MSnbase_2.31.1.tgz(r-4.4-arm64)MSnbase_2.31.1.tgz(r-4.4-x86_64)MSnbase_2.31.1.tgz(r-4.3-arm64)MSnbase_2.31.1.tgz(r-4.3-x86_64)
MSnbase_2.31.1.tar.gz(r-4.5-noble)MSnbase_2.31.1.tar.gz(r-4.4-noble)
MSnbase_2.31.1.tgz(r-4.4-emscripten)MSnbase_2.31.1.tgz(r-4.3-emscripten)
MSnbase.pdf |MSnbase.html✨
MSnbase/json (API)
| # Install 'MSnbase' in R: |
| install.packages('MSnbase', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lgatto/msnbase/issues
Datasets:
- TMT10 - TMT 6/10-plex sets
- TMT10ETD - TMT 6/10-plex sets
- TMT10HCD - TMT 6/10-plex sets
- TMT11 - TMT 6/10-plex sets
- TMT11HCD - TMT 6/10-plex sets
- TMT16 - TMT 6/10-plex sets
- TMT16HCD - TMT 6/10-plex sets
- TMT6 - TMT 6/10-plex sets
- TMT6b - TMT 6/10-plex sets
- TMT7 - TMT 6/10-plex sets
- TMT7b - TMT 6/10-plex sets
- iTRAQ4 - ITRAQ 4-plex set
- iTRAQ5 - ITRAQ 4-plex set
- iTRAQ8 - ITRAQ 4-plex set
- iTRAQ9 - ITRAQ 4-plex set
- itraqdata - Example 'MSnExp' and 'MSnSet' data sets
- msnset - Example 'MSnExp' and 'MSnSet' data sets
- msnset2 - Example 'MSnExp' and 'MSnSet' data sets
- naset - Quantitative proteomics data imputation
On BioConductor:MSnbase-2.31.0(bioc 3.20)MSnbase-2.30.1(bioc 3.19)
Last updated 2 months agofrom:d2b734ee72
Exports:abstractacquisitionNumaddFeaturesOfInterestaddIdentificationDataaddMSnSetMetadataaggregationFunaggvaralignRtall.equalanalyseranalyserDetailsanalyzeranalyzerDetailsas.data.frame.MSnExpas.data.frame.MSnSetas.data.frame.mzRidentas.data.frame.Spectrumas.ExpressionSet.MSnSetas.matrix.FoICollectionas.MIAME.MIAPEas.MSnExp.OnDiskMSnExpas.MSnSet.ExpressionSetassayDataassayData<-averageMSnSetbinbpicalculateFragmentscentroidedcentroided<-chromatogramChromatogramcleancoercecollisionEnergycolnames<-combinecombineFeaturescombineSpectracombineSpectraMovingWindowcommentscommoncommonFeatureNamescompareChromatogramscompareMSnSetscompareSpectracompfnamesconsensusSpectrumdescriptiondetectorTypedroplevels.MSnSetestimateMzResolutionestimateMzScatteringestimateNoiseexpandFeatureVarsexpemailexperimentData<-exprsexptitleextractPrecSpectraextractSpectraDatafactorsAsStringsfDatafData<-featureCVfeatureNamesfeatureNames<-FeaturesOfInterestfileNamefileNamesfillUpfilterAcquisitionNumfilterEmptySpectrafilterFilefilterIdentificationDataFramefilterIntensityfilterIsolationWindowfilterMsLevelfilterMzfilterNAfilterPolarityfilterPrecursorMzfilterPrecursorScanfilterRtfilterZerofnamesInfoiFoICollectionformatRtfromFilefvarLabelsgetEcolsgrepEcolshasChromatogramshasSpectraheaderidSummaryimageimage2imputeinstrumentCustomisationsinstrumentManufacturerinstrumentModelintensityionCountionSourceionSourceDetailsis.na.MSnSetisCentroidedisCentroidedFromFileisEmptyisMSnbaseFastLoadisMSnbaseVerboseisolationWindowLowerMzisolationWindowUpperMzlistOfmakeCamelCasemakeImpuritiesMatrixmakeMTDmakeNaDatamakeNaData2makePEPmakePRTMAplotMChromatogramsmeanMzIntsmergeFeatureVarsmetadatamoleculeEvidencemoleculeFeaturesms2dfmsInfomsLevelmsMapMSmapMSnbaseOptionsMSnSetMSnSetListmsnsetsMSpectramultiLabelsmultiplexmzmzResMzTabmzTabModemzTabTypenaplotnFeaturesnormalisenormalizenpcvnQuantsobjlogpDatapData<-peaksCountphenoDataphenoData<-pickPeaksplotplot2dplot3DplotDensityplotMzDeltaplotNApolarityprecScanNumprecSelectionprecSelectionTableprecursorChargeprecursorIntensityprecursorMzprocessingDataproductMzpsmspurityCorrectqualquantifyreadMgfDatareadMSDatareadMSData2readMSnSetreadMSnSet2readMzIdDatareadMzTabDatareadMzTabData_v0.9readSRMDatareduceremoveMultipleAssignmentremoveNoIdremovePeaksremoveReportersreporterColorsreporterColoursreporterNamesreporterNames<-requiredFvarLabelsrmFeaturesOfInterestrtimesampleNamessampleNames<-scalescanIndexselectFeatureDatasetMSnbaseFastLoadsetMSnbaseParallelThreshsetMSnbaseVerboseshowsmallMoleculessmoothsmoothedsmoothed<-spectraspectrapplysplitsplitByFilett.MSnSettictopNtransformIntensitytrimMztrimwsunique1unique2updateFeatureNamesupdateFvarLabelsupdateObjectupdateSampleNamesvalidateOnDiskMSnExpwhichNAwidthwrite.exprswriteMgfDatawriteMSDatawriteMzTabData
Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbslibcachemcliclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDelayedArraydigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMsCoreUtilsMultiAssayExperimentmunsellmzIDmzRncdf4nlmeopensslpcaMethodspillarpkgconfigplotlyplyrpreprocessCorepromisesProtGenericsPSMatchpurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2Rhdf5librlangrmarkdownS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitevsnwithrxfunXMLXVectoryamlzlibbioc
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Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Adds Identification Data | addIdentificationData addIdentificationData-methods |
| Identify aggregation outliers | aggvar |
| Coerce identification data to a 'data.frame' | as as.data.frame.mzRident |
| Generate an average 'MSnSet' | averageMSnSet |
| Bin 'MSnExp' or 'Spectrum' instances | bin bin-methods |
| Calculate ions produced by fragmentation. | calculateFragments calculateFragments,character,missing-method |
| Representation of chromatographic MS data | aggregationFun alignRt,Chromatogram,Chromatogram-method as.data.frame,Chromatogram-method bin,Chromatogram-method Chromatogram Chromatogram-class clean,Chromatogram-method compareChromatograms compareChromatograms,Chromatogram,Chromatogram-method filterIntensity,Chromatogram-method filterRt,Chromatogram-method fromFile,Chromatogram-method intensity,Chromatogram-method isEmpty,Chromatogram-method length,Chromatogram-method msLevel,Chromatogram-method mz,Chromatogram-method normalize,Chromatogram-method plot,Chromatogram,ANY-method precursorMz,Chromatogram-method productMz,Chromatogram-method rtime,Chromatogram-method show,Chromatogram-method transformIntensity transformIntensity,Chromatogram-method |
| Extract chromatogram object(s) | chromatogram chromatogram,MSnExp-method |
| Clean 'MSnExp', 'Spectrum' or 'Chromatogram' instances | clean clean-methods |
| Combines features in an 'MSnSet' object | combineFeatures combineFeatures,MSnSet-method |
| Combine Spectra | combineSpectra combineSpectra,MSnExp-method combineSpectra,MSpectra-method |
| Combine signal from consecutive spectra of LCMS experiments | combineSpectraMovingWindow |
| Keep only common feature names | commonFeatureNames |
| Compare two MSnSets | compareMSnSets |
| Compare Spectra of an 'MSnExp' or 'Spectrum' instances | compareSpectra compareSpectra-methods |
| Combine spectra to a consensus spectrum | consensusSpectrum |
| Estimate the m/z resolution of a spectrum | estimateMzResolution estimateMzResolution,MSnExp-method estimateMzResolution,Spectrum-method |
| Estimate m/z scattering in consecutive scans | estimateMzScattering |
| Noise Estimation for 'Spectrum' instances | estimateNoise estimateNoise-methods |
| Expand or merge feature variables | expandFeatureVars mergeFeatureVars |
| Extracts precursor-specific spectra from an 'MSnExp' object | extractPrecSpectra extractPrecSpectra-methods |
| Extract data from MSnbase objects for use in Spectra | extractSpectraData |
| Converts factors to strings | factorsAsStrings |
| Class '"FeatComp"' | common common,FeatComp-method common,methods compfnames compfnames,list,missing-method compfnames,MSnSet,MSnSet-method compfnames-methods FeatComp-class names,FeatComp-method show,FeatComp-method unique1 unique1,FeatComp-method unique1,methods unique2 unique2,FeatComp-method unique2,methods |
| Calculates coeffivient of variation for features | featureCV |
| Features of Interest | addFeaturesOfInterest addFeaturesOfInterest,FeaturesOfInterest,FoICollection-method addFeaturesOfInterest-methods as.matrix.FoICollection coerce,FoICollection,matrix-method description,FeaturesOfInterest-method description,FoICollection-method FeaturesOfInterest FeaturesOfInterest,character,character,missing-method FeaturesOfInterest,character,character,MSnSet-method FeaturesOfInterest-class FeaturesOfInterest-methods fnamesIn fnamesIn,FeaturesOfInterest,data.frame-method fnamesIn,FeaturesOfInterest,matrix-method fnamesIn,FeaturesOfInterest,MSnSet-method fnamesIn-methods foi foi,FeaturesOfInterest-method foi,FoICollection-method foi-methods FoICollection FoICollection,list-method FoICollection,missing-method FoICollection-class FoICollection-methods length,FeaturesOfInterest-method length,FoICollection-method lengths,FoICollection-method names,FoICollection-method names<-,FoICollection,character-method rmFeaturesOfInterest rmFeaturesOfInterest,FoICollection,numeric-method rmFeaturesOfInterest-methods show,FeaturesOfInterest-method show,FoICollection-method [,FoICollection,ANY,ANY,ANY-method [,FoICollection,ANY,ANY-method [,FoICollection-method [[,FoICollection,ANY,ANY-method [[,FoICollection-method |
| Fills up a vector | fillUp |
| Filter out unreliable PSMs. | filterIdentificationDataFrame |
| Format Retention Time | formatRt |
| Return a variable name | getVariableName |
| Returns the matching column names of indices. | getEcols grepEcols |
| Checks if raw data files have any spectra or chromatograms | hasChromatograms hasSpectra |
| NA heatmap visualisation for 2 groups | imageNA2 |
| Quantitative proteomics data imputation | impute,MSnSet-method naset |
| iPQF: iTRAQ (and TMT) Protein Quantification based on Features | iPQF |
| Get mode from mzML data file | isCentroidedFromFile |
| iTRAQ 4-plex set | iTRAQ4 iTRAQ5 iTRAQ8 iTRAQ9 |
| Example 'MSnExp' and 'MSnSet' data sets | itraqdata msnset msnset2 |
| Tests equality of list elements class | listOf |
| Convert to camel case by replacing dots by captial letters | makeCamelCase |
| Create a data with missing values | makeNaData makeNaData2 whichNA |
| Container for multiple Chromatogram objects | $,MChromatograms-method $<-,MChromatograms-method alignRt,MChromatograms,Chromatogram-method bin,MChromatograms-method c,MChromatograms-method clean,MChromatograms-method coerce,matrix,MChromatograms-method colnames<-,MChromatograms,ANY-method colnames<-,MChromatograms-method compareChromatograms,MChromatograms,MChromatograms-method compareChromatograms,MChromatograms,missing-method fData,MChromatograms-method fData<-,MChromatograms,ANY-method featureData,MChromatograms-method featureData<-,MChromatograms,ANY-method featureNames,MChromatograms-method featureNames<-,MChromatograms-method filterIntensity,MChromatograms-method fvarLabels,MChromatograms-method isEmpty,MChromatograms-method MChromatograms MChromatograms-class mz,MChromatograms-method normalize,MChromatograms-method pData,MChromatograms-method pData<-,MChromatograms,data.frame-method phenoData,MChromatograms-method plot,MChromatograms,ANY-method polarity,MChromatograms-method precursorMz,MChromatograms-method productMz,MChromatograms-method rownames<-,MChromatograms-method sampleNames,MChromatograms-method sampleNames<-,MChromatograms,ANY-method show,MChromatograms-method transformIntensity,MChromatograms-method [,MChromatograms,ANY,ANY,ANY-method [<-,MChromatograms,ANY,ANY,ANY-method [<-,MChromatograms-method |
| Combine a list of spectra to a single spectrum | meanMzInts |
| The "MIAPE" Class for Storing Proteomics Experiment Information | abstract,MIAPE-method analyser analyser,MIAPE-method analyserDetails analyserDetails,MIAPE-method analyzer analyzer,MIAPE-method analyzerDetails analyzerDetails,MIAPE-method as.MIAME.MIAPE class:MIAPE coerce,MIAPE,MIAME-method combine,MIAPE,MIAPE-method detectorType detectorType,MIAPE-method expemail expemail,MIAPE-method expinfo,MIAPE-method exptitle exptitle,MIAPE-method instrumentCustomisations instrumentCustomisations,MIAPE-method instrumentManufacturer instrumentManufacturer,MIAPE-method instrumentModel instrumentModel,MIAPE-method ionSource ionSource,MIAPE-method ionSourceDetails ionSourceDetails,MIAPE-method MIAPE MIAPE-class msInfo msInfo,MIAPE-method notes,MIAPE-method notes<-,MIAPE-method otherInfo,MIAPE-method pubMedIds,MIAPE-method pubMedIds<-,MIAPE-method samples,MIAPE-method show,MIAPE-method |
| Documenting missing data visualisation | missing-data missingdata |
| Class 'MSmap' | coerce,MSmap,data.frame-method dim,MSmap-method fileName,MSmap-method fileNames,MSmap-method msLevel,MSmap-method MSmap msMap msMap,MSmap-method MSmap,mzRpwiz-method MSmap,mzRramp-method MSmap,mzRraw-method MSmap,OnDiskMSnExp-method MSmap-class MSmap-method mz,MSmap-method mzRes mzRes,MSmap-method ncol,MSmap-method nrow,MSmap-method plot,MSmap,missing-method plot3D plot3D,MSmap-method rtime,MSmap-method show,MSmap-method t,MSmap-method |
| MSnbase options | isMSnbaseFastLoad isMSnbaseVerbose MSnbaseOptions setMSnbaseFastLoad setMSnbaseParallelThresh setMSnbaseVerbose |
| The 'MSnExp' Class for MS Data And Meta-Data | addIdentificationData,MSnExp,character-method addIdentificationData,MSnExp,data.frame-method addIdentificationData,MSnExp,mzID-method addIdentificationData,MSnExp,mzIDClasses-method addIdentificationData,MSnExp,mzIDCollection-method addIdentificationData,MSnExp,mzRident-method all.equal,MSnExp,MSnExp-method all.equal,MSnExp,OnDiskMSnExp-method all.equal,OnDiskMSnExp,MSnExp-method all.equal,OnDiskMSnExp,OnDiskMSnExp-method as.data.frame.MSnExp bin,MSnExp-method class:MSnExp clean,MSnExp-method coerce,MSnExp,data.frame-method coerce,MSnExp,MSpectra-method compareSpectra,MSnExp,missing-method estimateNoise,MSnExp-method extractPrecSpectra,MSnExp,numeric-method extractPrecSpectra,MSnExp-method filterAcquisitionNum filterAcquisitionNum,MSnExp-method filterAcquisitionNum,OnDiskMSnExp-method filterEmptySpectra filterEmptySpectra,MSnExp-method filterEmptySpectra,OnDiskMSnExp-method filterFile filterFile,MSnExp-method filterFile,OnDiskMSnExp-method filterIsolationWindow filterIsolationWindow,MSnExp-method filterMsLevel filterMsLevel,MSnExp-method filterMsLevel,OnDiskMSnExp-method filterMz,MSnExp-method filterMz,OnDiskMSnExp-method filterPolarity filterPolarity,MSnExp-method filterPolarity,OnDiskMSnExp-method filterPrecursorMz filterPrecursorMz,MSnExp-method filterPrecursorScan filterPrecursorScan,MSnExp-method filterPrecursorScan,OnDiskMSnExp-method filterRt filterRt,MSnExp-method filterRt,OnDiskMSnExp-method idSummary,MSnExp-method isCentroided,MSnExp-method isolationWindow,MSnExp-method MSnExp MSnExp-class pickPeaks,MSnExp-method plot,MSnExp plot,MSnExp,missing-method quantify,MSnExp,character-method quantify,MSnExp-method quantify,OnMSnExp-method removeMultipleAssignment,MSnExp-method removeNoId,MSnExp-method removePeaks,MSnExp-method removeReporters,MSnExp-method removeReporters,OnDiskMSnExp-method show,MSnExp-method smooth,MSnExp-method spectra,MSnExp-method splitByFile splitByFile,MSnExp,factor-method splitByFile,OnDiskMSnExp,factor-method trimMz,MSnExp,numeric-method trimMz,MSnExp-method |
| The "MSnProcess" Class | class:MSnProcess coerce,MSnProcess,list-method combine,MSnProcess,MSnProcess-method fileNames,MSnProcess-method MSnProcess MSnProcess-class show,MSnProcess-method |
| The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | acquisitionNum,MSnSet-method addIdentificationData,MSnSet,character-method addIdentificationData,MSnSet,data.frame-method addIdentificationData,MSnSet,mzID-method addIdentificationData,MSnSet,mzIDClasses-method addIdentificationData,MSnSet,mzIDCollection-method addIdentificationData,MSnSet,mzRident-method addMSnSetMetadata analyser,MSnSet-method analyzer,MSnSet-method as.data.frame.MSnSet as.ExpressionSet.MSnSet as.MSnSet.ExpressionSet class:MSnSet coerce,ExpressionSet,MSnSet-method coerce,IBSpectra,MSnSet-method coerce,MSnSet,data.frame-method coerce,MSnSet,ExpressionSet-method coerce,MSnSet,SummarizedExperiment-method coerce,SummarizedExperiment,MSnSet-method combine,MSnSet,MSnSet-method description,MSnSet-method detectorType,MSnSet-method dim,MSnSet-method droplevels.MSnSet expemail,MSnSet-method experimentData<-,MSnSet,MIAPE-method exprs,MSnSet-method exptitle,MSnSet-method fData<-,MSnSet,data.frame-method fileNames,MSnSet-method filterMsLevel,MSnSet-method filterNA filterNA,matrix-method filterNA,MSnSet-method filterZero filterZero,matrix-method filterZero,MSnSet-method fromFile,MSnSet-method idSummary idSummary,MSnSet-method image,MSnSet-method image2 ionSource,MSnSet-method log,MSnSet-method MAplot,MSnSet-method meanSdPlot,MSnSet-method ms2df msInfo,MSnSet-method MSnSet MSnSet-class pData<-,MSnSet,data.frame-method processingData,MSnSet-method purityCorrect,MSnSet,matrix-method purityCorrect,MSnSet-method qual qual,MSnSet-method removeMultipleAssignment removeMultipleAssignment,MSnSet-method removeMultipleAssignment-method removeNoId,MSnSet-method show,MSnSet-method t.MSnSet topN topN,matrix-method topN,MSnSet,MSnSet-method topN,MSnSet-method trimws trimws,data.frame-method trimws,MSnSet-method updateFeatureNames updateFvarLabels updateSampleNames write.exprs write.exprs,MSnSet-method [,MSnSet,ANY,ANY,ANY-method [,MSnSet,ANY,ANY-method [,MSnSet-method |
| Storing multiple related MSnSets | fData,MSnSetList-method fData<-,MSnSetList,DataFrame-method lapply,MSnSetList-method length,MSnSetList-method MSnSetList MSnSetList-class msnsets names,MSnSetList-method names<-,MSnSetList,ANY-method objlog sapply,MSnSetList-method show,MSnSetList-method split,MSnSet,character-method split,MSnSet,factor-method unsplit,MSnSetList,factor-method [,MSnSetList,ANY,ANY,ANY-method [,MSnSetList,ANY,missing,missing-method [[,MSnSetList,ANY,ANY-method [[,MSnSetList,ANY,missing-method |
| List of Spectrum objects along with annotations | acquisitionNum,MSpectra-method centroided,MSpectra-method clean,MSpectra-method coerce,MSpectra,list-method coerce,MSpectra,MSnExp-method collisionEnergy,MSpectra-method filterMsLevel,MSpectra-method filterMz,MSpectra-method fromFile,MSpectra-method intensity,MSpectra-method ionCount,MSpectra-method isCentroided,MSpectra-method isEmpty,MSpectra-method msLevel,MSpectra-method MSpectra MSpectra-class mz,MSpectra-method peaksCount,MSpectra,ANY-method pickPeaks,MSpectra-method polarity,MSpectra-method precScanNum,MSpectra-method precursorCharge,MSpectra-method precursorIntensity,MSpectra-method precursorMz,MSpectra-method removePeaks,MSpectra-method rtime,MSpectra-method scanIndex,MSpectra-method show,MSpectra-method smooth,MSpectra-method smoothed,MSpectra-method tic,MSpectra-method writeMgfData,MSpectra-method |
| Parse 'MzTab' files | class:MzTab coerce,MzTab,MSnSetList-method comments fileName,MzTab-method fileNames,MzTab-method metadata,MzTab-method moleculeEvidence moleculeFeatures MzTab MzTab-class mzTabMode mzTabType peptides,MzTab-method proteins,MzTab-method psms,MzTab-method show,MzTab-method smallMolecules |
| Overview of missing value | naplot |
| Navigate an 'MSnExp' object | navMS nextMS prevMS |
| How many features in a group? | nFeatures |
| Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects | normalise normalise,MSnExp-method normalise,MSnSet-method normalise,Spectrum-method normalise,Spectrum2-method normalise-methods normalize normalize,MSnExp-method normalize,MSnSet-method normalize,Spectrum-method normalize,Spectrum2-method normalize-methods scale,MSnSet-method |
| Combine peptides into proteins. | normToReference NTR |
| Non-parametric coefficient of variation | npcv |
| Count the number of quantitfied features. | nQuants |
| The 'OnDiskMSnExp' Class for MS Data And Meta-Data | acquisitionNum,OnDiskMSnExp-method as.MSnExp.OnDiskMSnExp assayData,OnDiskMSnExp-method bin,OnDiskMSnExp-method bpi bpi,OnDiskMSnExp-method centroided,OnDiskMSnExp-method centroided<-,OnDiskMSnExp,logical-method class:OnDiskMSnExp clean,OnDiskMSnExp-method coerce,OnDiskMSnExp,MSnExp-method collisionEnergy,OnDiskMSnExp-method compareSpectra,OnDiskMSnExp,missing-method estimateNoise,OnDiskMSnExp-method extractPrecSpectra,OnDiskMSnExp,numeric-method featureNames,OnDiskMSnExp-method featureNames<-,OnDiskMSnExp,ANY-method featureNames<-,OnDiskMSnExp-method fromFile,OnDiskMSnExp-method header,OnDiskMSnExp,missing-method header,OnDiskMSnExp,numeric-method intensity,OnDiskMSnExp-method ionCount,OnDiskMSnExp-method isCentroided,OnDiskMSnExp-method isolationWindowLowerMz,OnDiskMSnExp-method isolationWindowUpperMz,OnDiskMSnExp-method length,OnDiskMSnExp-method msLevel,OnDiskMSnExp-method mz,OnDiskMSnExp-method normalise,OnDiskMSnExp-method normalize,OnDiskMSnExp-method OnDiskMSnExp OnDiskMSnExp-class peaksCount,OnDiskMSnExp,missing-method peaksCount,OnDiskMSnExp,numeric-method pickPeaks,OnDiskMSnExp-method polarity,OnDiskMSnExp-method precScanNum,OnDiskMSnExp-method precursorCharge,OnDiskMSnExp-method precursorIntensity,OnDiskMSnExp-method precursorMz,OnDiskMSnExp-method quantify,OnDiskMSnExp-method removePeaks,OnDiskMSnExp-method rtime,OnDiskMSnExp-method scanIndex,OnDiskMSnExp-method show,OnDiskMSnExp-method smooth,OnDiskMSnExp-method smoothed,OnDiskMSnExp-method smoothed<-,OnDiskMSnExp,logical-method spectra,OnDiskMSnExp-method spectrapply,OnDiskMSnExp-method tic,OnDiskMSnExp-method trimMz,OnDiskMSnExp,numeric-method validateOnDiskMSnExp [,OnDiskMSnExp,ANY,ANY,ANY-method [,OnDiskMSnExp,logicalOrNumeric,missing,missing-method [[,OnDiskMSnExp,ANY,ANY,missing-method [[,OnDiskMSnExp,ANY,ANY-method [[,OnDiskMSnExp,ANY,missing,missing-method [[,OnDiskMSnExp-method |
| Peak Detection for 'MSnExp' or 'Spectrum' instances | pickPeaks pickPeaks-methods |
| Plotting 'MSnExp' and 'Spectrum' object(s) | plot plot,Spectrum,missing-method plot,Spectrum-method plot,Spectrum2,character-method plot-methods plot.MSnExp plot.Spectrum plot.Spectrum.character |
| Plotting a 'Spectrum' vs another 'Spectrum' object. | plot,Spectrum,Spectrum-method plot.Spectrum.Spectrum |
| The 'plot2d' method for 'MSnExp' quality assessment | plot2d plot2d,data.frame-method plot2d,MSnExp-method plot2d-methods |
| The 'plotDensity' method for 'MSnExp' quality assessment | plotDensity plotDensity,data.frame-method plotDensity,MSnExp-method plotDensity-methods |
| The delta m/z plot | plotMzDelta plotMzDelta,MSnExp-method plotMzDelta,mzRramp-method plotMzDelta-methods |
| Exploring missing data in 'MSnSet' instances | is.na.MSnSet plotNA plotNA,matrix-method plotNA,MSnSet-method plotNA-methods |
| Number of precursor selection events | precSelection precSelectionTable |
| Simple processing step class | executeProcessingStep ProcessingStep ProcessingStep-class ProcessingStep:OnDiskMSnExp show,ProcessingStep-method |
| Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | $,pSet-method $<-,pSet-method abstract,pSet-method acquisitionNum,pSet-method analyser,pSet-method analyserDetails,pSet-method analyzer,pSet-method analyzerDetails,pSet-method assayData,pSet-method centroided,pSet-method centroided<-,pSet,ANY-method centroided<-,pSet,logical-method class:pSet coerce,AnnotatedDataFrame,list-method coerce,MIAxE,list-method collisionEnergy,pSet-method description,pSet-method detectorType,pSet-method dim dim,pSet-method expemail,pSet-method experimentData,pSet-method exptitle,pSet-method fData,pSet-method fData<-,pSet,data.frame-method featureData,pSet-method featureNames,pSet-method fileNames fileNames,pSet-method fromFile,pSet-method fvarLabels,pSet-method fvarMetadata,pSet-method header header,pSet,missing-method header,pSet,numeric-method instrumentCustomisations,pSet-method instrumentManufacturer,pSet-method instrumentModel,pSet-method intensity,pSet-method ionCount,pSet-method ionSource,pSet-method ionSourceDetails,pSet-method isolationWindowLowerMz isolationWindowLowerMz,pSet-method isolationWindowUpperMz isolationWindowUpperMz,pSet-method length length,pSet-method 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 precAcquisitionNum,pSet-method precScanNum,pSet-method precursorCharge,pSet-method precursorIntensity,pSet-method precursorMz,pSet-method processingData processingData,pSet-method protocolData,pSet-method pSet pSet-class pubMedIds,pSet-method rtime,pSet-method sampleNames,pSet-method sampleNames<-,pSet,character-method scanIndex,pSet-method smoothed,pSet-method smoothed<-,pSet,ANY-method smoothed<-,pSet,logical-method spectra spectra,pSet-method spectrapply spectrapply,pSet-method tic,pSet-method varLabels,pSet-method varMetadata,pSet-method [,pSet,ANY,ANY,ANY-method [,pSet,ANY,ANY-method [,pSet-method [[,pSet,ANY,ANY-method [[,pSet-method |
| Performs reporter ions purity correction | makeImpuritiesMatrix purityCorrect purityCorrect-methods |
| Quantifies 'MSnExp' and 'Spectrum' objects | quantify quantify-methods |
| Import mgf files as 'MSnExp' instances. | readMgfData |
| Imports mass-spectrometry raw data files as 'MSnExp' instances. | readMSData readMSData2 |
| Read 'MSnSet' | readMSnSet readMSnSet2 |
| Import peptide-spectrum matches | coerce,mzRident,data.frame-method readMzIdData |
| Read an 'mzTab' file | readMzTabData |
| Read an 'mzTab' file | readMzTabData_v0.9 |
| Read SRM/MRM chromatographic data | readSRMData |
| Reduce a data.frame | reduce,data.frame-method |
| Removes non-identified features | removeNoId removeNoId-methods |
| Removes low intensity peaks | removePeaks removePeaks-methods |
| Removes reporter ion tag peaks | removeReporters removeReporters-methods |
| The "ReporterIons" Class | class:ReporterIons description,ReporterIons-method length,ReporterIons-method length-method mz,ReporterIons-method names,ReporterIons-method reporterColors reporterColors,ReporterIons-method reporterColors-method reporterColours reporterColours,ReporterIons-method reporterColours-method ReporterIons ReporterIons-class reporterNames reporterNames,ReporterIons-method reporterNames-method reporterNames<- reporterNames<-,ReporterIons,ANY-method reporterNames<-,ReporterIons,character-method reporterNames<-,ReporterIons-method show,ReporterIons-method width width,ReporterIons-method width-method [,ReporterIons,ANY,ANY,ANY-method [,ReporterIons,ANY,ANY-method [,ReporterIons-method |
| Select feature variables of interest | requiredFvarLabels selectFeatureData |
| Smooths 'MSnExp' or 'Spectrum' instances | smooth smooth-methods |
| The "Spectrum" Class | acquisitionNum acquisitionNum,Spectrum-method as.data.frame.Spectrum bin,Spectrum-method centroided centroided,Spectrum-method centroided<- centroided<-,Spectrum,ANY-method centroided<-,Spectrum,logical-method class:Spectrum clean,Spectrum-method coerce,Spectrum,data.frame-method compareSpectra,Spectrum,Spectrum-method estimateNoise,Spectrum-method filtermz,Spectrum,numeric-method filterMz,Spectrum-method fromFile fromFile,Spectrum-method intensity intensity,Spectrum-method ionCount ionCount,Spectrum-method isCentroided isCentroided,Spectrum-method isEmpty,environment-method isEmpty,Spectrum-method msLevel msLevel,Spectrum-method mz mz,Spectrum-method peaksCount peaksCount,Spectrum,missing-method pickPeaks,Spectrum-method polarity polarity,Spectrum-method quantify,Spectrum,character-method quantify,Spectrum-method removePeaks,Spectrum-method rtime rtime,Spectrum-method scanIndex scanIndex,Spectrum-method show,Spectrum-method smooth,Spectrum-method smoothed smoothed,Spectrum-method smoothed<- smoothed<-,Spectrum,ANY-method smoothed<-,Spectrum,logical-method Spectrum Spectrum-class tic tic,Spectrum-method trimMz,Spectrum,numeric-method trimMz,Spectrum-method |
| The "Spectrum1" Class for MS1 Spectra | class:Spectrum1 Spectrum1 Spectrum1-class |
| The "Spectrum2" Class for MSn Spectra | calculateFragments,character,Spectrum2-method class:Spectrum2 collisionEnergy collisionEnergy,Spectrum-method precAcquisitionNum precAcquisitionNum,Spectrum-method precScanNum precScanNum,Spectrum-method precursorCharge precursorCharge,Spectrum-method precursorIntensity precursorIntensity,Spectrum-method precursorMz precursorMz,Spectrum-method removeReporters,Spectrum-method Spectrum2 Spectrum2-class |
| TMT 6/10-plex sets | TMT10 TMT10ETD TMT10HCD TMT11 TMT11HCD TMT16 TMT16HCD TMT6 TMT6b TMT7 TMT7b |
| Trims 'MSnExp' or 'Spectrum' instances | filterMz filterMz-methods trimMz trimMz-methods |
| Update MSnbase objects | updateObject,MSnExp-method updateObject,Spectrum-method |
| Write an experiment or spectrum to an mgf file | writeMgfData writeMgfData,MSnExp-method writeMgfData,Spectrum-method writeMgfData-methods |
| Write MS data to mzML or mzXML files | writeMSData writeMSData,MSnExp,character-method |
| Export an MzTab object as mzTab file. | writeMzTabData |
