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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| acquisitionNum-method | List of Spectrum objects along with annotations |
| 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 |
| 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 |
| 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| centroided-method | List of Spectrum objects along with annotations |
| 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) |
| Chromatograms | Container for multiple Chromatogram objects |
| Chromatograms-class | Container for multiple Chromatogram objects |
| 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| clean-method | List of Spectrum objects along with annotations |
| clean-method | The "Spectrum" Class |
| clean-methods | Clean 'MSnExp', 'Spectrum' or 'Chromatogram' instances |
| coerce-method | Container for multiple Chromatogram objects |
| coerce-method | Features of Interest |
| 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 | Parse 'MzTab' files |
| coerce-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| coerce-method | List of Spectrum objects along with annotations |
| coerce-method | The "Spectrum" Class |
| 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| collisionEnergy-method | List of Spectrum objects along with annotations |
| 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 |
| 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 |
| defaultNeutralLoss | Calculate ions produced by fragmentation. |
| 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 |
| 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. |
| 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| fromFile-method | List of Spectrum objects along with annotations |
| 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 |
| get.amino.acids | Amino acids |
| get.atomic.mass | Atomic mass. |
| 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 | Quantitative proteomics data imputation |
| impute-method | Quantitative proteomics data imputation |
| impute-methods | Quantitative proteomics data imputation |
| imputeMethods | 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| intensity-method | List of Spectrum objects along with annotations |
| intensity-method | The "Spectrum" Class |
| intensity-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
| ionCount | The "Spectrum" Class |
| ionCount-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| ionCount-method | List of Spectrum objects along with annotations |
| 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| isCentroided-method | List of Spectrum objects along with annotations |
| 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 |
| 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 |
| 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| msLevel-method | List of Spectrum objects along with annotations |
| 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 |
| mz | The "Spectrum" Class |
| mz-method | Representation of chromatographic MS data |
| mz-method | Container for multiple Chromatogram objects |
| mz-method | Class 'MSmap' |
| mz-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| mz-method | The "ReporterIons" Class |
| mz-method | List of Spectrum objects along with annotations |
| 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 |
| navMS | Navigate an 'MSnExp' object |
| ncol-method | Class 'MSmap' |
| nextMS | Navigate an 'MSnExp' object |
| 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 | 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| peaksCount-method | List of Spectrum objects along with annotations |
| 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| pickPeaks-method | List of Spectrum objects along with annotations |
| 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| polarity-method | List of Spectrum objects along with annotations |
| 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| precScanNum-method | List of Spectrum objects along with annotations |
| 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| precursorCharge-method | List of Spectrum objects along with annotations |
| 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| precursorIntensity-method | List of Spectrum objects along with annotations |
| 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| precursorMz-method | List of Spectrum objects along with annotations |
| precursorMz-method | The "Spectrum2" Class for MSn Spectra |
| precursorMz-method | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
| prevMS | Navigate an 'MSnExp' object |
| 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 | Representation of chromatographic MS data |
| 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| removePeaks-method | List of Spectrum objects along with annotations |
| 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| rtime-method | List of Spectrum objects along with annotations |
| 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| scanIndex-method | List of Spectrum objects along with annotations |
| 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 | Container for multiple Chromatogram objects |
| show-method | Class '"FeatComp"' |
| show-method | Features of Interest |
| 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 | 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 | List of Spectrum objects along with annotations |
| 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| smooth-method | List of Spectrum objects along with annotations |
| smooth-method | The "Spectrum" Class |
| smooth-methods | Smooths 'MSnExp' or 'Spectrum' instances |
| smoothed | The "Spectrum" Class |
| smoothed-method | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| smoothed-method | List of Spectrum objects along with annotations |
| 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 | List of Spectrum objects along with annotations |
| spectra | Class to Contain Raw Mass-Spectrometry Assays and Experimental Metadata |
| Spectra-class | List of Spectrum objects along with annotations |
| 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 | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| tic-method | List of Spectrum objects along with annotations |
| 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 |
| 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 |
| 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 | Container for multiple Chromatogram objects |
| [-method | Features of Interest |
| [-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 |