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"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" ] }, { "page": "chromatogram-MSnExp-method", "title": "Extract chromatogram object(s)", "topics": [ "chromatogram", "chromatogram,MSnExp-method" ] }, { "page": "clean-methods", "title": "Clean 'MSnExp', 'Spectrum' or 'Chromatogram' instances", "topics": [ "clean", "clean-methods" ] }, { "page": "combineFeatures", "title": "Combines features in an 'MSnSet' object", "topics": [ "combineFeatures", "combineFeatures,MSnSet-method" ] }, { "page": "combineSpectra", "title": "Combine Spectra", "topics": [ "combineSpectra", "combineSpectra,MSnExp-method", "combineSpectra,MSpectra-method" ] }, { "page": "combineSpectraMovingWindow", "title": "Combine signal from consecutive spectra of LCMS experiments", "topics": [ "combineSpectraMovingWindow" ] }, { "page": "commonFeatureNames", "title": "Keep only common feature names", "topics": [ "commonFeatureNames" ] }, { "page": "compareMSnSets", "title": "Compare two MSnSets", "topics": [ "compareMSnSets" ] }, { "page": "compareSpectra-methods", "title": "Compare Spectra of an 'MSnExp' or 'Spectrum' instances", "topics": [ "compareSpectra", "compareSpectra-methods" ] }, { "page": "consensusSpectrum", "title": "Combine spectra to a consensus spectrum", "concept": [ "spectra combination functions" ], "topics": [ "consensusSpectrum" ] }, { "page": "estimateMzResolution", "title": "Estimate the m/z resolution of a spectrum", "topics": [ "estimateMzResolution", "estimateMzResolution,MSnExp-method", "estimateMzResolution,Spectrum-method" ] }, { "page": "estimateMzScattering", "title": "Estimate m/z scattering in consecutive scans", "topics": [ "estimateMzScattering" ] }, { "page": "estimateNoise-method", "title": "Noise Estimation for 'Spectrum' instances", "topics": [ "estimateNoise", "estimateNoise-methods" ] }, { "page": "fData-utils", "title": "Expand or merge feature variables", "topics": [ "expandFeatureVars", "mergeFeatureVars" ] }, { "page": "extractPrecSpectra-methods", "title": "Extracts precursor-specific spectra from an 'MSnExp' object", "topics": [ "extractPrecSpectra", "extractPrecSpectra-methods" ] }, { "page": "extractSpectraData", "title": "Conversion between objects from the Spectra and MSnbase packages", "topics": [ "coerce,Spectra,MSpectra-method", "extractSpectraData" ] }, { "page": "factorsAsStrings", "title": "Converts factors to strings", "topics": [ "factorsAsStrings" ] }, { "page": "FeatComp-class", "title": "Class '\"FeatComp\"'", "topics": [ "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" ] }, { "page": "featureCV", "title": "Calculates coeffivient of variation for features", "topics": [ "featureCV" ] }, { "page": "FeaturesOfInterest-class", "title": "Features of Interest", "topics": [ "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" ] }, { "page": "fillUp", "title": "Fills up a vector", "topics": [ "fillUp" ] }, { "page": "filterIdentificationDataFrame", "title": "Filter out unreliable PSMs.", "topics": [ "filterIdentificationDataFrame" ] }, { "page": "formatRt", "title": "Format Retention Time", "topics": [ "formatRt" ] }, { "page": "getVariableName", "title": "Return a variable name", "topics": [ "getVariableName" ] }, { "page": "grepEcols", "title": "Returns the matching column names of indices.", "topics": [ "getEcols", "grepEcols" ] }, { "page": "hasSpectraOrChromatograms", "title": "Checks if raw data files have any spectra or chromatograms", "topics": [ "hasChromatograms", "hasSpectra" ] }, { "page": "imageNA2", "title": "NA heatmap visualisation for 2 groups", "topics": [ "imageNA2" ] }, { "page": "impute", "title": "Quantitative proteomics data imputation", "topics": [ "impute,MSnSet-method", "naset" ] }, { "page": "iPQF", "title": "iPQF: iTRAQ (and TMT) Protein Quantification based on Features", "topics": [ "iPQF" ] }, { "page": "isCentroidedFromFile", "title": "Get mode from mzML data file", "topics": [ "isCentroidedFromFile" ] }, { "page": "iTRAQ4", "title": "iTRAQ 4-plex set", "topics": [ "iTRAQ4", "iTRAQ5", "iTRAQ8", "iTRAQ9" ] }, { "page": "itraqdata", "title": "Example 'MSnExp' and 'MSnSet' data sets", "topics": [ "itraqdata", "msnset", "msnset2" ] }, { "page": "listOf", "title": "Tests equality of list elements class", "topics": [ "listOf" ] }, { "page": "makeCamelCase", "title": "Convert to camel case by replacing dots by captial letters", "topics": [ "makeCamelCase" ] }, { "page": "makeNaData", "title": "Create a data with missing values", "topics": [ "makeNaData", "makeNaData2", "whichNA" ] }, { "page": "MChromatograms-class", "title": "Container for multiple Chromatogram objects", "topics": [ "$,MChromatograms-method", "$<-,MChromatograms-method", "alignRt,MChromatograms,Chromatogram-method", "bin,MChromatograms-method", "c,MChromatograms-method", "clean,MChromatograms-method", "coerce,matrix,MChromatograms-method", "colnames<-,MChromatograms,ANY-method", "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" ] }, { "page": "meanMzInts", "title": "Combine a list of spectra to a single spectrum", "concept": [ "spectra combination functions" ], "topics": [ "meanMzInts" ] }, { "page": "MIAPE-class", "title": "The \"MIAPE\" Class for Storing Proteomics Experiment Information", "topics": [ "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" ] }, { "page": "missing-data", "title": "Documenting missing data visualisation", "topics": [ "missing-data", "missingdata" ] }, { "page": "MSmap-class", "title": "Class 'MSmap'", "topics": [ "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" ] }, { "page": "MSnbaseOptions", "title": "MSnbase options", "topics": [ "isMSnbaseFastLoad", "isMSnbaseVerbose", "MSnbaseOptions", "setMSnbaseFastLoad", "setMSnbaseParallelThresh", "setMSnbaseVerbose" ] }, { "page": "MSnExp-class", "title": "The 'MSnExp' Class for MS Data And Meta-Data", "concept": [ "MSnExp" ], "topics": [ "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" ] }, { "page": "MSnProcess-class", "title": "The \"MSnProcess\" Class", "topics": [ "class:MSnProcess", "coerce,MSnProcess,list-method", "combine,MSnProcess,MSnProcess-method", "fileNames,MSnProcess-method", "MSnProcess", "MSnProcess-class", "show,MSnProcess-method" ] }, { "page": "MSnSet-class", "title": "The \"MSnSet\" Class for MS Proteomics Expression Data and Meta-Data", "topics": [ "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" ] }, { "page": "MSnSetList-class", "title": "Storing multiple related MSnSets", "topics": [ "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" ] }, { "page": "MSpectra", "title": "List of Spectrum objects along with annotations", "topics": [ "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" ] }, { "page": "MzTab-class", "title": "Parse 'MzTab' files", "topics": [ "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" ] }, { "page": "naplot", "title": "Overview of missing value", "topics": [ "naplot" ] }, { "page": "nFeatures", "title": "How many features in a group?", "topics": [ "nFeatures" ] }, { "page": "normalise-methods", "title": "Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects", "topics": [ "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" ] }, { "page": "normToReference", "title": "Combine peptides into proteins.", "topics": [ "normToReference", "NTR" ] }, { "page": "npcv", "title": "Non-parametric coefficient of variation", "topics": [ "npcv" ] }, { "page": "nQuants", "title": "Count the number of quantitfied features.", "topics": [ "nQuants" ] }, { "page": "OnDiskMSnExp-class", "title": "The 'OnDiskMSnExp' Class for MS Data And Meta-Data", "concept": [ "OnDiskMSnExp" ], "topics": [ "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" ] }, { "page": "pickPeaks-method", "title": "Peak Detection for 'MSnExp' or 'Spectrum' instances", "topics": [ "pickPeaks", "pickPeaks-methods" ] }, { "page": "plot-methods", "title": "Plotting 'MSnExp' and 'Spectrum' object(s)", "topics": [ "plot", "plot,Spectrum,missing-method", "plot,Spectrum-method", "plot,Spectrum2,character-method", "plot-methods", "plot.MSnExp", "plot.Spectrum", "plot.Spectrum.character" ] }, { "page": "plotSpectrumSpectrum-methods", "title": "Plotting a 'Spectrum' vs another 'Spectrum' object.", "topics": [ "plot,Spectrum,Spectrum-method", "plot.Spectrum.Spectrum" ] }, { "page": "plot2d-methods", "title": "The 'plot2d' method for 'MSnExp' quality assessment", "topics": [ "plot2d", "plot2d,data.frame-method", "plot2d,MSnExp-method", "plot2d-methods" ] }, { "page": "plotDensity-methods", "title": "The 'plotDensity' method for 'MSnExp' quality assessment", "topics": [ "plotDensity", "plotDensity,data.frame-method", "plotDensity,MSnExp-method", "plotDensity-methods" ] }, { "page": "plotMzDelta-methods", "title": "The delta m/z plot", "topics": [ "plotMzDelta", "plotMzDelta,MSnExp-method", "plotMzDelta,mzRramp-method", "plotMzDelta-methods" ] }, { "page": "plotNA-methods", "title": "Exploring missing data in 'MSnSet' instances", "topics": [ "is.na.MSnSet", "plotNA", "plotNA,matrix-method", "plotNA,MSnSet-method", "plotNA-methods" ] }, { "page": "precSelection", "title": "Number of precursor selection events", "topics": [ "precSelection", "precSelectionTable" ] }, { "page": "ProcessingStep-class", "title": "Simple processing step class", "concept": [ "ProcessingStep" ], "topics": [ "executeProcessingStep", "ProcessingStep", "ProcessingStep-class", "ProcessingStep:OnDiskMSnExp", "show,ProcessingStep-method" ] }, { "page": "pSet-class", "title": "Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata", "topics": [ "$,pSet-method", "$<-,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" ] }, { "page": "purityCorrect-methods", "title": "Performs reporter ions purity correction", "topics": [ "makeImpuritiesMatrix", "purityCorrect", "purityCorrect-methods" ] }, { "page": "quantify-methods", "title": "Quantifies 'MSnExp' and 'Spectrum' objects", "topics": [ "quantify", "quantify-methods" ] }, { "page": "readMgfData", "title": "Import mgf files as 'MSnExp' instances.", "topics": [ "readMgfData" ] }, { "page": "readMSData", "title": "Imports mass-spectrometry raw data files as 'MSnExp' instances.", "topics": [ "readMSData", "readMSData2" ] }, { "page": "readMSnSet", "title": "Read 'MSnSet'", "topics": [ "readMSnSet", "readMSnSet2" ] }, { "page": "readMzIdData", "title": "Import peptide-spectrum matches", "topics": [ "coerce,mzRident,data.frame-method", "readMzIdData" ] }, { "page": "readMzTabData", "title": "Read an 'mzTab' file", "topics": [ "readMzTabData" ] }, { "page": "readMzTabData_v0.9", "title": "Read an 'mzTab' file", "topics": [ "readMzTabData_v0.9" ] }, { "page": "readSRMData", "title": "Read SRM/MRM chromatographic data", "topics": [ "readSRMData" ] }, { "page": "reduce-data.frame-method", "title": "Reduce a data.frame", "topics": [ "reduce,data.frame-method" ] }, { "page": "removeNoId-methods", "title": "Removes non-identified features", "topics": [ "removeNoId", "removeNoId-methods" ] }, { "page": "removePeaks-methods", "title": "Removes low intensity peaks", "topics": [ "removePeaks", "removePeaks-methods" ] }, { "page": "removeReporters-methods", "title": "Removes reporter ion tag peaks", "topics": [ "removeReporters", "removeReporters-methods" ] }, { "page": "ReporterIons-class", "title": "The \"ReporterIons\" Class", "topics": [ "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" ] }, { "page": "selectFeatureData", "title": "Select feature variables of interest", "topics": [ "requiredFvarLabels", "selectFeatureData" ] }, { "page": "smooth-methods", "title": "Smooths 'MSnExp' or 'Spectrum' instances", "topics": [ "smooth", "smooth-methods" ] }, { "page": "Spectrum-class", "title": "The \"Spectrum\" Class", "topics": [ "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" ] }, { "page": "Spectrum1-class", "title": "The \"Spectrum1\" Class for MS1 Spectra", "topics": [ "class:Spectrum1", "Spectrum1", "Spectrum1-class" ] }, { "page": "Spectrum2-class", "title": "The \"Spectrum2\" Class for MSn Spectra", "topics": [ "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" ] }, { "page": "TMT6", "title": "TMT 6/10-plex sets", "topics": [ "TMT10", "TMT10ETD", "TMT10HCD", "TMT11", "TMT11HCD", "TMT16", "TMT16HCD", "TMT6", "TMT6b", "TMT7", "TMT7b" ] }, { "page": "trimMz-methods", "title": "Trims 'MSnExp' or 'Spectrum' instances", "topics": [ "filterMz", "filterMz-methods", "trimMz", "trimMz-methods" ] }, { "page": "updateObject-methods", "title": "Update MSnbase objects", "topics": [ "updateObject,MSnExp-method", "updateObject,Spectrum-method" ] }, { "page": "writeMgfData-methods", "title": "Write an experiment or spectrum to an mgf file", "topics": [ "writeMgfData", "writeMgfData,MSnExp-method", "writeMgfData,Spectrum-method", "writeMgfData-methods" ] }, { "page": "writeMSData", "title": "Write MS data to mzML or mzXML files", "topics": [ "writeMSData", "writeMSData,MSnExp,character-method" ] }, { "page": "writeMzTabData", "title": "Export an MzTab object as mzTab file.", "topics": [ "writeMzTabData" ] } ], "_readme": "https://github.com/bioc/MSnbase/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "affy", "affyio", "AnnotationFilter", "askpass", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "biocmake", "BiocManager", "BiocParallel", "bslib", "cachem", "cli", "clue", "cluster", "codetools", "cpp11", "crosstalk", "curl", "data.table", "DelayedArray", "digest", "dir.expiry", "doParallel", "dplyr", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "foreach", 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tags", "Chromatogram and MChromatograms: classes to handle chromatographic data", "Other classes", "Lists of MSnSet instances", "Miscellaneous", "Unit tests", "Processing methods", "Session information", "References" ], "created": "2018-08-21 10:26:49", "modified": "2020-06-18 14:29:46", "commits": 4 }, { "source": "v01-MSnbase-demo.Rmd", "filename": "v01-MSnbase-demo.html", "title": "MSnbase: MS data processing, visualisation and quantification", "author": "Laurent Gatto, Johannes Rainer, Sebastian Gibb", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Speed and memory requirements", "Data structure and content", "Importing experiments", "Exporting experiments/MS data", "MS experiments", "Spectra objects", "Reporter ions", "Chromatogram objects", "Plotting raw data", "MS data space", "MS Spectra", "MS Chromatogram", "Tandem MS identification data", "Adding identification data", "Filtering identification data", "Calculate Fragments", "Quality control", "Raw data 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