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"fields": [], "table": false, "tojson": false }, { "name": "TMT10", "title": "TMT 6/10-plex sets", "object": "TMT10", "class": [ "ReporterIons" ], "fields": [], "table": false, "tojson": false }, { "name": "TMT10ETD", "title": "TMT 6/10-plex sets", "object": "TMT10ETD", "class": [ "ReporterIons" ], "fields": [], "table": false, "tojson": false }, { "name": "TMT10HCD", "title": "TMT 6/10-plex sets", "object": "TMT10HCD", "class": [ "ReporterIons" ], "fields": [], "table": false, "tojson": false }, { "name": "TMT11", "title": "TMT 6/10-plex sets", "object": "TMT11", "class": [ "ReporterIons" ], "fields": [], "table": false, "tojson": false }, { "name": "TMT11HCD", "title": "TMT 6/10-plex sets", "object": "TMT11HCD", "class": [ "ReporterIons" ], "fields": [], "table": false, "tojson": false }, { "name": "TMT16", "title": "TMT 6/10-plex sets", "object": "TMT16", "class": [ "ReporterIons" ], "fields": [], "table": false, "tojson": false }, { "name": "TMT16HCD", "title": "TMT 6/10-plex sets", "object": "TMT16HCD", "class": [ "ReporterIons" ], "fields": [], "table": false, "tojson": false }, { "name": "TMT6", "title": "TMT 6/10-plex sets", "object": "TMT6", "class": [ "ReporterIons" ], "fields": [], "table": false, "tojson": false }, { "name": "TMT6b", "title": "TMT 6/10-plex sets", "object": "TMT6b", "class": [ "ReporterIons" ], "fields": [], "table": false, "tojson": false }, { "name": "TMT7", "title": "TMT 6/10-plex sets", "object": "TMT7", "class": [ "ReporterIons" ], "fields": [], "table": false, "tojson": false }, { "name": "TMT7b", "title": "TMT 6/10-plex sets", "object": "TMT7b", "class": [ "ReporterIons" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "addIdentificationData-methods", "title": "Adds Identification Data", "topics": [ "addIdentificationData", "addIdentificationData-methods" ] }, { "page": "aggvar", "title": "Identify aggregation outliers", "topics": [ "aggvar" ] }, { "page": "mzRident2dfr", "title": "Coerce identification data to a 'data.frame'", "topics": [ "as", "as.data.frame.mzRident" ] }, { "page": "averageMSnSet", "title": "Generate an average 'MSnSet'", "topics": [ "averageMSnSet" ] }, { "page": "bin-methods", "title": "Bin 'MSnExp' or 'Spectrum' instances", "topics": [ "bin", "bin-methods" ] }, { "page": "calculateFragments-methods", "title": "Calculate ions produced by fragmentation.", "topics": [ "calculateFragments", "calculateFragments,character,missing-method" ] }, { "page": "Chromatogram-class", "title": "Representation of chromatographic MS data", "topics": [ "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" ] }, { "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/HEAD/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", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "highr", "htmltools", "htmlwidgets", "httr", "igraph", "impute", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "knitr", "labeling", 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"_vignettes": [ { "source": "v05-MSnbase-development.Rmd", "filename": "v05-MSnbase-development.html", "title": "A short introduction to MSnbase development", "author": "Laurent Gatto, Johannes Rainer, Sebastian Gibb", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Coding style", "r Biocpkg(\"MSnbase\") classes", "pSet: a virtual class for raw mass spectrometry data and meta data", "MSnExp: a class for MS experiments", "OnDiskMSnExp: a on-disk implementation of the MSnExp class", "MSnSet: a class for quantitative proteomics data", "MSnProcess: a class for logging processing meta data", "MIAPE: Minimum Information About a Proteomics Experiment", "Spectrum et al.: classes for MS spectra", "ReporterIons: a class for isobaric 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 processing", "Cleaning spectra", "Spectrum processing", "MS2 isobaric tagging quantitation", "Reporter ions quantitation", "Importing quantitation data", "Importing chromatographic data from SRM/MRM experiments", "Peak adjustments", "Processing quantitative data", "Data imputation", "Normalisation", "Feature aggregation", "Label-free MS2 quantitation", "Peptide counting", "Spectral counting and intensity methods", "Spectra comparison", "Plotting two spectra", "Comparison metrics", "Quantitative assessment of incomplete dissociation", "Combining MSnSet instances", "Combining identical samples", "Combine different samples", "Splitting and unsplitting MSnSet instances", "Averaging MSnSet instances", "MS^E^ data processing", "Session information", "References" ], "created": "2018-08-21 10:26:49", "modified": "2026-04-08 22:01:44", "commits": 7 }, { "source": "v04-benchmarking.Rmd", "filename": "v04-benchmarking.html", "title": "MSnbase benchmarking", "author": "Laurent Gatto, Johannes Rainer", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Benchmarking", "Reading data", "Data size", "Accessing spectra", "MS2 quantitation", "Notable differences on-disk and in-memory implementations", "MS levels", "Serialisation", "Data processing", "Validity", "Conclusions" ], "created": "2018-08-21 10:26:49", "modified": "2026-03-17 21:05:03", "commits": 4 }, { "source": "v02-MSnbase-io.Rmd", "filename": "v02-MSnbase-io.html", "title": "MSnbase IO capabilities", "author": "Laurent Gatto", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Data input", "Raw data", "Peak lists", "Quantitation data", "Data output", "RData files", "mzML/mzXML files", "Creating MSnSet from text spread sheets", "A complete work flow", "The MSnSet class", "A shorter work flow", "Session information", "References" ], "created": "2018-08-21 10:26:49", "modified": "2020-06-18 14:29:46", "commits": 3 }, { "source": "v03-MSnbase-centroiding.Rmd", "filename": "v03-MSnbase-centroiding.html", "title": "MSnbase: centroiding of profile-mode MS data", "author": "Johannes Rainer", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Centroiding of profile-mode MS data", "Improving the signal quality", "Data smoothing", "Refinement of the centroid's 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