A B C D E F G H I L M N O P Q R S T U V W misc
| abstract-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| abstract-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| acquisitionNum | The "Spectrum" Class | 
| acquisitionNum-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| acquisitionNum-method | List of Spectrum objects along with annotations | 
| acquisitionNum-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| acquisitionNum-method | The "Spectrum" Class | 
| acquisitionNum-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| addFeaturesOfInterest | Features of Interest | 
| addFeaturesOfInterest-method | Features of Interest | 
| addFeaturesOfInterest-methods | Features of Interest | 
| addIdentificationData | Adds Identification Data | 
| addIdentificationData-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| addIdentificationData-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| addIdentificationData-methods | Adds Identification Data | 
| addMSnSetMetadata | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| aggregationFun | Representation of chromatographic MS data | 
| aggvar | Identify aggregation outliers | 
| alignRt-method | Representation of chromatographic MS data | 
| alignRt-method | Container for multiple Chromatogram objects | 
| all.equal-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| analyser | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| analyser-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| analyser-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| analyser-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| analyserDetails | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| analyserDetails-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| analyserDetails-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| analyzer | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| analyzer-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| analyzer-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| analyzer-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| analyzerDetails | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| analyzerDetails-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| analyzerDetails-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| as | Coerce identification data to a 'data.frame' | 
| as.data.frame-method | Representation of chromatographic MS data | 
| as.data.frame.MSnExp | The 'MSnExp' Class for MS Data And Meta-Data | 
| as.data.frame.MSnSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| as.data.frame.mzRident | Coerce identification data to a 'data.frame' | 
| as.data.frame.Spectrum | The "Spectrum" Class | 
| as.ExpressionSet.MSnSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| as.matrix.FoICollection | Features of Interest | 
| as.MIAME.MIAPE | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| as.MSnExp.OnDiskMSnExp | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| as.MSnSet.ExpressionSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| assayData-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| assayData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| averageMSnSet | Generate an average 'MSnSet' | 
| bin | Bin 'MSnExp' or 'Spectrum' instances | 
| bin-method | Representation of chromatographic MS data | 
| bin-method | Container for multiple Chromatogram objects | 
| bin-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| bin-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| bin-method | The "Spectrum" Class | 
| bin-methods | Bin 'MSnExp' or 'Spectrum' instances | 
| bpi | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| bpi-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| c-method | Container for multiple Chromatogram objects | 
| calculateFragments | Calculate ions produced by fragmentation. | 
| calculateFragments-method | The "Spectrum2" Class for MSn Spectra | 
| calculateFragments-method | Calculate ions produced by fragmentation. | 
| centroided | The "Spectrum" Class | 
| centroided-method | List of Spectrum objects along with annotations | 
| centroided-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| centroided-method | The "Spectrum" Class | 
| centroided-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| centroided<- | The "Spectrum" Class | 
| centroided<--method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| centroided<--method | The "Spectrum" Class | 
| centroided<--method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| Chromatogram | Representation of chromatographic MS data | 
| chromatogram | Extract chromatogram object(s) | 
| Chromatogram-class | Representation of chromatographic MS data | 
| chromatogram-method | Extract chromatogram object(s) | 
| class:MIAPE | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| class:MSnExp | The 'MSnExp' Class for MS Data And Meta-Data | 
| class:MSnProcess | The "MSnProcess" Class | 
| class:MSnSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| class:MzTab | Parse 'MzTab' files | 
| class:OnDiskMSnExp | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| class:pSet | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| class:ReporterIons | The "ReporterIons" Class | 
| class:Spectrum | The "Spectrum" Class | 
| class:Spectrum1 | The "Spectrum1" Class for MS1 Spectra | 
| class:Spectrum2 | The "Spectrum2" Class for MSn Spectra | 
| clean | Clean 'MSnExp', 'Spectrum' or 'Chromatogram' instances | 
| clean-method | Representation of chromatographic MS data | 
| clean-method | Container for multiple Chromatogram objects | 
| clean-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| clean-method | List of Spectrum objects along with annotations | 
| clean-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| clean-method | The "Spectrum" Class | 
| clean-methods | Clean 'MSnExp', 'Spectrum' or 'Chromatogram' instances | 
| coerce-method | Features of Interest | 
| coerce-method | Container for multiple Chromatogram objects | 
| coerce-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| coerce-method | Class 'MSmap' | 
| coerce-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| coerce-method | The "MSnProcess" Class | 
| coerce-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| coerce-method | List of Spectrum objects along with annotations | 
| coerce-method | Parse 'MzTab' files | 
| coerce-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| coerce-method | The "Spectrum" Class | 
| coerce-method | Conversion between objects from the Spectra and MSnbase packages | 
| coerce-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| coerce-method | Import peptide-spectrum matches | 
| collisionEnergy | The "Spectrum2" Class for MSn Spectra | 
| collisionEnergy-method | List of Spectrum objects along with annotations | 
| collisionEnergy-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| collisionEnergy-method | The "Spectrum2" Class for MSn Spectra | 
| collisionEnergy-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| colnames<--method | Container for multiple Chromatogram objects | 
| combine-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| combine-method | The "MSnProcess" Class | 
| combine-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| combineFeatures | Combines features in an 'MSnSet' object | 
| combineFeatures-method | Combines features in an 'MSnSet' object | 
| combineSpectra | Combine Spectra | 
| combineSpectra-method | Combine Spectra | 
| combineSpectraMovingWindow | Combine signal from consecutive spectra of LCMS experiments | 
| comments | Parse 'MzTab' files | 
| common | Class '"FeatComp"' | 
| common,methods | Class '"FeatComp"' | 
| common-method | Class '"FeatComp"' | 
| commonFeatureNames | Keep only common feature names | 
| compareChromatograms | Representation of chromatographic MS data | 
| compareChromatograms-method | Representation of chromatographic MS data | 
| compareChromatograms-method | Container for multiple Chromatogram objects | 
| compareMSnSets | Compare two MSnSets | 
| compareSpectra | Compare Spectra of an 'MSnExp' or 'Spectrum' instances | 
| compareSpectra-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| compareSpectra-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| compareSpectra-method | The "Spectrum" Class | 
| compareSpectra-methods | Compare Spectra of an 'MSnExp' or 'Spectrum' instances | 
| compfnames | Class '"FeatComp"' | 
| compfnames-method | Class '"FeatComp"' | 
| compfnames-methods | Class '"FeatComp"' | 
| consensusSpectrum | Combine spectra to a consensus spectrum | 
| description-method | Features of Interest | 
| description-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| description-method | The "ReporterIons" Class | 
| description-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| detectorType | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| detectorType-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| detectorType-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| detectorType-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| dim | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| dim-method | Class 'MSmap' | 
| dim-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| dim-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| droplevels.MSnSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| estimateMzResolution | Estimate the m/z resolution of a spectrum | 
| estimateMzResolution-method | Estimate the m/z resolution of a spectrum | 
| estimateMzScattering | Estimate m/z scattering in consecutive scans | 
| estimateNoise | Noise Estimation for 'Spectrum' instances | 
| estimateNoise-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| estimateNoise-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| estimateNoise-method | The "Spectrum" Class | 
| estimateNoise-methods | Noise Estimation for 'Spectrum' instances | 
| executeProcessingStep | Simple processing step class | 
| expandFeatureVars | Expand or merge feature variables | 
| expemail | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| expemail-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| expemail-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| expemail-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| experimentData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| experimentData<--method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| expinfo-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| exprs-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| exptitle | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| exptitle-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| exptitle-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| exptitle-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| extractPrecSpectra | Extracts precursor-specific spectra from an 'MSnExp' object | 
| extractPrecSpectra-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| extractPrecSpectra-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| extractPrecSpectra-methods | Extracts precursor-specific spectra from an 'MSnExp' object | 
| extractSpectraData | Conversion between objects from the Spectra and MSnbase packages | 
| factorsAsStrings | Converts factors to strings | 
| fData-method | Container for multiple Chromatogram objects | 
| fData-method | Storing multiple related MSnSets | 
| fData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| fData<--method | Container for multiple Chromatogram objects | 
| fData<--method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| fData<--method | Storing multiple related MSnSets | 
| fData<--method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| FeatComp-class | Class '"FeatComp"' | 
| featureCV | Calculates coeffivient of variation for features | 
| featureData-method | Container for multiple Chromatogram objects | 
| featureData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| featureData<--method | Container for multiple Chromatogram objects | 
| featureNames-method | Container for multiple Chromatogram objects | 
| featureNames-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| featureNames-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| featureNames<--method | Container for multiple Chromatogram objects | 
| featureNames<--method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| FeaturesOfInterest | Features of Interest | 
| FeaturesOfInterest-class | Features of Interest | 
| FeaturesOfInterest-method | Features of Interest | 
| FeaturesOfInterest-methods | Features of Interest | 
| fileName-method | Class 'MSmap' | 
| fileName-method | Parse 'MzTab' files | 
| fileNames | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| fileNames-method | Class 'MSmap' | 
| fileNames-method | The "MSnProcess" Class | 
| fileNames-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| fileNames-method | Parse 'MzTab' files | 
| fileNames-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| fillUp | Fills up a vector | 
| filterAcquisitionNum | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterAcquisitionNum-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterEmptySpectra | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterEmptySpectra-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterFile | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterFile-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterIdentificationDataFrame | Filter out unreliable PSMs. | 
| filterIntensity-method | Representation of chromatographic MS data | 
| filterIntensity-method | Container for multiple Chromatogram objects | 
| filterIsolationWindow | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterIsolationWindow-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterMsLevel | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterMsLevel-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterMsLevel-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| filterMsLevel-method | List of Spectrum objects along with annotations | 
| filterMz | Trims 'MSnExp' or 'Spectrum' instances | 
| filterMz-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterMz-method | List of Spectrum objects along with annotations | 
| filterMz-method | The "Spectrum" Class | 
| filtermz-method | The "Spectrum" Class | 
| filterMz-methods | Trims 'MSnExp' or 'Spectrum' instances | 
| filterNA | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| filterNA-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| filterPolarity | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterPolarity-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterPrecursorMz | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterPrecursorMz-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterPrecursorScan | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterPrecursorScan-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterRt | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterRt-method | Representation of chromatographic MS data | 
| filterRt-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| filterZero | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| filterZero-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| fnamesIn | Features of Interest | 
| fnamesIn-method | Features of Interest | 
| fnamesIn-methods | Features of Interest | 
| foi | Features of Interest | 
| foi-method | Features of Interest | 
| foi-methods | Features of Interest | 
| FoICollection | Features of Interest | 
| FoICollection-class | Features of Interest | 
| FoICollection-method | Features of Interest | 
| FoICollection-methods | Features of Interest | 
| formatRt | Format Retention Time | 
| fromFile | The "Spectrum" Class | 
| fromFile-method | Representation of chromatographic MS data | 
| fromFile-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| fromFile-method | List of Spectrum objects along with annotations | 
| fromFile-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| fromFile-method | The "Spectrum" Class | 
| fromFile-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| fvarLabels-method | Container for multiple Chromatogram objects | 
| fvarLabels-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| fvarMetadata-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| getEcols | Returns the matching column names of indices. | 
| getVariableName | Return a variable name | 
| grepEcols | Returns the matching column names of indices. | 
| hasChromatograms | Checks if raw data files have any spectra or chromatograms | 
| hasSpectra | Checks if raw data files have any spectra or chromatograms | 
| header | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| header-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| header-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| idSummary | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| idSummary-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| idSummary-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| image-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| image2 | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| imageNA2 | NA heatmap visualisation for 2 groups | 
| impute-method | Quantitative proteomics data imputation | 
| instrumentCustomisations | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| instrumentCustomisations-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| instrumentCustomisations-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| instrumentManufacturer | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| instrumentManufacturer-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| instrumentManufacturer-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| instrumentModel | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| instrumentModel-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| instrumentModel-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| intensity | The "Spectrum" Class | 
| intensity-method | Representation of chromatographic MS data | 
| intensity-method | List of Spectrum objects along with annotations | 
| intensity-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| intensity-method | The "Spectrum" Class | 
| intensity-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| ionCount | The "Spectrum" Class | 
| ionCount-method | List of Spectrum objects along with annotations | 
| ionCount-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| ionCount-method | The "Spectrum" Class | 
| ionCount-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| ionSource | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| ionSource-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| ionSource-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| ionSource-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| ionSourceDetails | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| ionSourceDetails-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| ionSourceDetails-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| iPQF | iPQF: iTRAQ (and TMT) Protein Quantification based on Features | 
| is.na.MSnSet | Exploring missing data in 'MSnSet' instances | 
| isCentroided | The "Spectrum" Class | 
| isCentroided-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| isCentroided-method | List of Spectrum objects along with annotations | 
| isCentroided-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| isCentroided-method | The "Spectrum" Class | 
| isCentroidedFromFile | Get mode from mzML data file | 
| isEmpty-method | Representation of chromatographic MS data | 
| isEmpty-method | Container for multiple Chromatogram objects | 
| isEmpty-method | List of Spectrum objects along with annotations | 
| isEmpty-method | The "Spectrum" Class | 
| isMSnbaseFastLoad | MSnbase options | 
| isMSnbaseVerbose | MSnbase options | 
| isolationWindow-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| isolationWindowLowerMz | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| isolationWindowLowerMz-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| isolationWindowLowerMz-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| isolationWindowUpperMz | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| isolationWindowUpperMz-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| isolationWindowUpperMz-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| 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 | 
| lapply-method | Storing multiple related MSnSets | 
| length | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| length-method | Representation of chromatographic MS data | 
| length-method | Features of Interest | 
| length-method | Storing multiple related MSnSets | 
| length-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| length-method | The "ReporterIons" Class | 
| length-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| lengths-method | Features of Interest | 
| listOf | Tests equality of list elements class | 
| log-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| makeCamelCase | Convert to camel case by replacing dots by captial letters | 
| makeImpuritiesMatrix | Performs reporter ions purity correction | 
| makeNaData | Create a data with missing values | 
| makeNaData2 | Create a data with missing values | 
| MAplot-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| MChromatograms | Container for multiple Chromatogram objects | 
| MChromatograms-class | Container for multiple Chromatogram objects | 
| meanMzInts | Combine a list of spectra to a single spectrum | 
| meanSdPlot-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| mergeFeatureVars | Expand or merge feature variables | 
| metadata-method | Parse 'MzTab' files | 
| MIAPE | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| MIAPE-class | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| missing-data | Documenting missing data visualisation | 
| missingdata | Documenting missing data visualisation | 
| moleculeEvidence | Parse 'MzTab' files | 
| moleculeFeatures | Parse 'MzTab' files | 
| ms2df | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| msInfo | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| msInfo-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| msInfo-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| msInfo-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| msLevel | The "Spectrum" Class | 
| msLevel-method | Representation of chromatographic MS data | 
| msLevel-method | Class 'MSmap' | 
| msLevel-method | List of Spectrum objects along with annotations | 
| msLevel-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| msLevel-method | The "Spectrum" Class | 
| msLevel-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| MSmap | Class 'MSmap' | 
| msMap | Class 'MSmap' | 
| MSmap-class | Class 'MSmap' | 
| MSmap-method | Class 'MSmap' | 
| msMap-method | Class 'MSmap' | 
| MSnbaseOptions | MSnbase options | 
| MSnExp | The 'MSnExp' Class for MS Data And Meta-Data | 
| MSnExp-class | The 'MSnExp' Class for MS Data And Meta-Data | 
| MSnProcess | The "MSnProcess" Class | 
| MSnProcess-class | The "MSnProcess" Class | 
| MSnSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| msnset | Example 'MSnExp' and 'MSnSet' data sets | 
| MSnSet-class | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| msnset2 | Example 'MSnExp' and 'MSnSet' data sets | 
| MSnSetList | Storing multiple related MSnSets | 
| MSnSetList-class | Storing multiple related MSnSets | 
| msnsets | Storing multiple related MSnSets | 
| MSpectra | List of Spectrum objects along with annotations | 
| MSpectra-class | List of Spectrum objects along with annotations | 
| mz | The "Spectrum" Class | 
| mz-method | Representation of chromatographic MS data | 
| mz-method | Container for multiple Chromatogram objects | 
| mz-method | Class 'MSmap' | 
| mz-method | List of Spectrum objects along with annotations | 
| mz-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| mz-method | The "ReporterIons" Class | 
| mz-method | The "Spectrum" Class | 
| mz-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| mzRes | Class 'MSmap' | 
| mzRes-method | Class 'MSmap' | 
| MzTab | Parse 'MzTab' files | 
| MzTab-class | Parse 'MzTab' files | 
| mzTabMode | Parse 'MzTab' files | 
| mzTabType | Parse 'MzTab' files | 
| names-method | Class '"FeatComp"' | 
| names-method | Features of Interest | 
| names-method | Storing multiple related MSnSets | 
| names-method | The "ReporterIons" Class | 
| names<--method | Features of Interest | 
| names<--method | Storing multiple related MSnSets | 
| naplot | Overview of missing value | 
| naset | Quantitative proteomics data imputation | 
| ncol-method | Class 'MSmap' | 
| nFeatures | How many features in a group? | 
| normalise | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects | 
| normalise-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| normalise-method | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects | 
| normalise-methods | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects | 
| normalize | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects | 
| normalize-method | Representation of chromatographic MS data | 
| normalize-method | Container for multiple Chromatogram objects | 
| normalize-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| normalize-method | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects | 
| normalize-methods | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects | 
| normToReference | Combine peptides into proteins. | 
| notes-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| notes-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| notes<--method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| npcv | Non-parametric coefficient of variation | 
| nQuants | Count the number of quantitfied features. | 
| nrow-method | Class 'MSmap' | 
| NTR | Combine peptides into proteins. | 
| objlog | Storing multiple related MSnSets | 
| OnDiskMSnExp | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| OnDiskMSnExp-class | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| otherInfo-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| pData-method | Container for multiple Chromatogram objects | 
| pData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| pData<--method | Container for multiple Chromatogram objects | 
| pData<--method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| pData<--method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| peaksCount | The "Spectrum" Class | 
| peaksCount-method | List of Spectrum objects along with annotations | 
| peaksCount-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| peaksCount-method | The "Spectrum" Class | 
| peaksCount-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| peptides-method | Parse 'MzTab' files | 
| phenoData-method | Container for multiple Chromatogram objects | 
| phenoData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| phenoData<--method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| pickPeaks | Peak Detection for 'MSnExp' or 'Spectrum' instances | 
| pickPeaks-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| pickPeaks-method | List of Spectrum objects along with annotations | 
| pickPeaks-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| pickPeaks-method | The "Spectrum" Class | 
| pickPeaks-methods | Peak Detection for 'MSnExp' or 'Spectrum' instances | 
| plot | Plotting 'MSnExp' and 'Spectrum' object(s) | 
| plot,MSnExp | The 'MSnExp' Class for MS Data And Meta-Data | 
| plot-method | Representation of chromatographic MS data | 
| plot-method | Container for multiple Chromatogram objects | 
| plot-method | Class 'MSmap' | 
| plot-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| plot-method | Plotting 'MSnExp' and 'Spectrum' object(s) | 
| plot-method | Plotting a 'Spectrum' vs another 'Spectrum' object. | 
| plot-methods | Plotting 'MSnExp' and 'Spectrum' object(s) | 
| plot.MSnExp | Plotting 'MSnExp' and 'Spectrum' object(s) | 
| plot.Spectrum | Plotting 'MSnExp' and 'Spectrum' object(s) | 
| plot.Spectrum.character | Plotting 'MSnExp' and 'Spectrum' object(s) | 
| plot.Spectrum.Spectrum | Plotting a 'Spectrum' vs another 'Spectrum' object. | 
| plot2d | The 'plot2d' method for 'MSnExp' quality assessment | 
| plot2d-method | The 'plot2d' method for 'MSnExp' quality assessment | 
| plot2d-methods | The 'plot2d' method for 'MSnExp' quality assessment | 
| plot3D | Class 'MSmap' | 
| plot3D-method | Class 'MSmap' | 
| plotDensity | The 'plotDensity' method for 'MSnExp' quality assessment | 
| plotDensity-method | The 'plotDensity' method for 'MSnExp' quality assessment | 
| plotDensity-methods | The 'plotDensity' method for 'MSnExp' quality assessment | 
| plotMzDelta | The delta m/z plot | 
| plotMzDelta-method | The delta m/z plot | 
| plotMzDelta-methods | The delta m/z plot | 
| plotNA | Exploring missing data in 'MSnSet' instances | 
| plotNA-method | Exploring missing data in 'MSnSet' instances | 
| plotNA-methods | Exploring missing data in 'MSnSet' instances | 
| polarity | The "Spectrum" Class | 
| polarity-method | Container for multiple Chromatogram objects | 
| polarity-method | List of Spectrum objects along with annotations | 
| polarity-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| polarity-method | The "Spectrum" Class | 
| polarity-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| precAcquisitionNum | The "Spectrum2" Class for MSn Spectra | 
| precAcquisitionNum-method | The "Spectrum2" Class for MSn Spectra | 
| precAcquisitionNum-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| precScanNum | The "Spectrum2" Class for MSn Spectra | 
| precScanNum-method | List of Spectrum objects along with annotations | 
| precScanNum-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| precScanNum-method | The "Spectrum2" Class for MSn Spectra | 
| precScanNum-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| precSelection | Number of precursor selection events | 
| precSelectionTable | Number of precursor selection events | 
| precursorCharge | The "Spectrum2" Class for MSn Spectra | 
| precursorCharge-method | List of Spectrum objects along with annotations | 
| precursorCharge-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| precursorCharge-method | The "Spectrum2" Class for MSn Spectra | 
| precursorCharge-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| precursorIntensity | The "Spectrum2" Class for MSn Spectra | 
| precursorIntensity-method | List of Spectrum objects along with annotations | 
| precursorIntensity-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| precursorIntensity-method | The "Spectrum2" Class for MSn Spectra | 
| precursorIntensity-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| precursorMz | The "Spectrum2" Class for MSn Spectra | 
| precursorMz-method | Representation of chromatographic MS data | 
| precursorMz-method | Container for multiple Chromatogram objects | 
| precursorMz-method | List of Spectrum objects along with annotations | 
| precursorMz-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| precursorMz-method | The "Spectrum2" Class for MSn Spectra | 
| precursorMz-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| processingData | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| processingData-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| processingData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| ProcessingStep | Simple processing step class | 
| ProcessingStep-class | Simple processing step class | 
| ProcessingStep:OnDiskMSnExp | Simple processing step class | 
| productMz-method | Representation of chromatographic MS data | 
| productMz-method | Container for multiple Chromatogram objects | 
| proteins-method | Parse 'MzTab' files | 
| protocolData-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| pSet | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| pSet-class | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| psms-method | Parse 'MzTab' files | 
| pubMedIds-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| pubMedIds-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| pubMedIds<--method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| purityCorrect | Performs reporter ions purity correction | 
| purityCorrect-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| purityCorrect-methods | Performs reporter ions purity correction | 
| qual | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| qual-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| quantify | Quantifies 'MSnExp' and 'Spectrum' objects | 
| quantify-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| quantify-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| quantify-method | The "Spectrum" Class | 
| quantify-methods | Quantifies 'MSnExp' and 'Spectrum' objects | 
| readMgfData | Import mgf files as 'MSnExp' instances. | 
| readMSData | Imports mass-spectrometry raw data files as 'MSnExp' instances. | 
| readMSData2 | Imports mass-spectrometry raw data files as 'MSnExp' instances. | 
| readMSnSet | Read 'MSnSet' | 
| readMSnSet2 | Read 'MSnSet' | 
| readMzIdData | Import peptide-spectrum matches | 
| readMzTabData | Read an 'mzTab' file | 
| readMzTabData_v0.9 | Read an 'mzTab' file | 
| readSRMData | Read SRM/MRM chromatographic data | 
| reduce-method | Reduce a data.frame | 
| removeMultipleAssignment | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| removeMultipleAssignment-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| removeMultipleAssignment-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| removeNoId | Removes non-identified features | 
| removeNoId-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| removeNoId-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| removeNoId-methods | Removes non-identified features | 
| removePeaks | Removes low intensity peaks | 
| removePeaks-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| removePeaks-method | List of Spectrum objects along with annotations | 
| removePeaks-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| removePeaks-method | The "Spectrum" Class | 
| removePeaks-methods | Removes low intensity peaks | 
| removeReporters | Removes reporter ion tag peaks | 
| removeReporters-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| removeReporters-method | The "Spectrum2" Class for MSn Spectra | 
| removeReporters-methods | Removes reporter ion tag peaks | 
| reporterColors | The "ReporterIons" Class | 
| reporterColors-method | The "ReporterIons" Class | 
| reporterColours | The "ReporterIons" Class | 
| reporterColours-method | The "ReporterIons" Class | 
| ReporterIons | The "ReporterIons" Class | 
| ReporterIons-class | The "ReporterIons" Class | 
| reporterNames | The "ReporterIons" Class | 
| reporterNames-method | The "ReporterIons" Class | 
| reporterNames<- | The "ReporterIons" Class | 
| reporterNames<--method | The "ReporterIons" Class | 
| requiredFvarLabels | Select feature variables of interest | 
| rmFeaturesOfInterest | Features of Interest | 
| rmFeaturesOfInterest-method | Features of Interest | 
| rmFeaturesOfInterest-methods | Features of Interest | 
| rownames<--method | Container for multiple Chromatogram objects | 
| rtime | The "Spectrum" Class | 
| rtime-method | Representation of chromatographic MS data | 
| rtime-method | Class 'MSmap' | 
| rtime-method | List of Spectrum objects along with annotations | 
| rtime-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| rtime-method | The "Spectrum" Class | 
| rtime-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| sampleNames-method | Container for multiple Chromatogram objects | 
| sampleNames-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| sampleNames<--method | Container for multiple Chromatogram objects | 
| sampleNames<--method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| samples-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| sapply-method | Storing multiple related MSnSets | 
| scale-method | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects | 
| scanIndex | The "Spectrum" Class | 
| scanIndex-method | List of Spectrum objects along with annotations | 
| scanIndex-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| scanIndex-method | The "Spectrum" Class | 
| scanIndex-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| selectFeatureData | Select feature variables of interest | 
| setMSnbaseFastLoad | MSnbase options | 
| setMSnbaseParallelThresh | MSnbase options | 
| setMSnbaseVerbose | MSnbase options | 
| show-method | Representation of chromatographic MS data | 
| show-method | Class '"FeatComp"' | 
| show-method | Features of Interest | 
| show-method | Container for multiple Chromatogram objects | 
| show-method | The "MIAPE" Class for Storing Proteomics Experiment Information | 
| show-method | Class 'MSmap' | 
| show-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| show-method | The "MSnProcess" Class | 
| show-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| show-method | Storing multiple related MSnSets | 
| show-method | List of Spectrum objects along with annotations | 
| show-method | Parse 'MzTab' files | 
| show-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| show-method | Simple processing step class | 
| show-method | The "ReporterIons" Class | 
| show-method | The "Spectrum" Class | 
| smallMolecules | Parse 'MzTab' files | 
| smooth | Smooths 'MSnExp' or 'Spectrum' instances | 
| smooth-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| smooth-method | List of Spectrum objects along with annotations | 
| smooth-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| smooth-method | The "Spectrum" Class | 
| smooth-methods | Smooths 'MSnExp' or 'Spectrum' instances | 
| smoothed | The "Spectrum" Class | 
| smoothed-method | List of Spectrum objects along with annotations | 
| smoothed-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| smoothed-method | The "Spectrum" Class | 
| smoothed-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| smoothed<- | The "Spectrum" Class | 
| smoothed<--method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| smoothed<--method | The "Spectrum" Class | 
| smoothed<--method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| spectra | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| spectra-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| spectra-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| spectra-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| spectrapply | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| spectrapply-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| spectrapply-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| Spectrum | The "Spectrum" Class | 
| Spectrum-class | The "Spectrum" Class | 
| Spectrum1 | The "Spectrum1" Class for MS1 Spectra | 
| Spectrum1-class | The "Spectrum1" Class for MS1 Spectra | 
| Spectrum2 | The "Spectrum2" Class for MSn Spectra | 
| Spectrum2-class | The "Spectrum2" Class for MSn Spectra | 
| split-method | Storing multiple related MSnSets | 
| splitByFile | The 'MSnExp' Class for MS Data And Meta-Data | 
| splitByFile-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| t-method | Class 'MSmap' | 
| t.MSnSet | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| tic | The "Spectrum" Class | 
| tic-method | List of Spectrum objects along with annotations | 
| tic-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| tic-method | The "Spectrum" Class | 
| tic-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| 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 | 
| topN | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| topN-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| transformIntensity | Representation of chromatographic MS data | 
| transformIntensity-method | Representation of chromatographic MS data | 
| transformIntensity-method | Container for multiple Chromatogram objects | 
| trimMz | Trims 'MSnExp' or 'Spectrum' instances | 
| trimMz-method | The 'MSnExp' Class for MS Data And Meta-Data | 
| trimMz-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| trimMz-method | The "Spectrum" Class | 
| trimMz-methods | Trims 'MSnExp' or 'Spectrum' instances | 
| trimws | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| trimws-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| unique1 | Class '"FeatComp"' | 
| unique1,methods | Class '"FeatComp"' | 
| unique1-method | Class '"FeatComp"' | 
| unique2 | Class '"FeatComp"' | 
| unique2,methods | Class '"FeatComp"' | 
| unique2-method | Class '"FeatComp"' | 
| unsplit-method | Storing multiple related MSnSets | 
| updateFeatureNames | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| updateFvarLabels | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| updateObject-method | Update MSnbase objects | 
| updateSampleNames | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| validateOnDiskMSnExp | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| varLabels-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| varMetadata-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| whichNA | Create a data with missing values | 
| width | The "ReporterIons" Class | 
| width-method | The "ReporterIons" Class | 
| write.exprs | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| write.exprs-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| writeMgfData | Write an experiment or spectrum to an mgf file | 
| writeMgfData-method | List of Spectrum objects along with annotations | 
| writeMgfData-method | Write an experiment or spectrum to an mgf file | 
| writeMgfData-methods | Write an experiment or spectrum to an mgf file | 
| writeMSData | Write MS data to mzML or mzXML files | 
| writeMSData-method | Write MS data to mzML or mzXML files | 
| writeMzTabData | Export an MzTab object as mzTab file. | 
| $-method | Container for multiple Chromatogram objects | 
| $-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| $<--method | Container for multiple Chromatogram objects | 
| $<--method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| [-method | Features of Interest | 
| [-method | Container for multiple Chromatogram objects | 
| [-method | The "MSnSet" Class for MS Proteomics Expression Data and Meta-Data | 
| [-method | Storing multiple related MSnSets | 
| [-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| [-method | The "ReporterIons" Class | 
| [-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata | 
| [<--method | Container for multiple Chromatogram objects | 
| [[-method | Features of Interest | 
| [[-method | Storing multiple related MSnSets | 
| [[-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data | 
| [[-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |