Man pages for lgatto/MSnbase
Base Functions and Classes for Mass Spectrometry and Proteomics
| addIdentificationData-methods | Adds Identification Data |
| aggvar | Identify aggregation outliers |
| averageMSnSet | Generate an average 'MSnSet' |
| bin-methods | Bin 'MSnExp' or 'Spectrum' instances |
| calculateFragments-methods | Calculate ions produced by fragmentation. |
| Chromatogram-class | Representation of chromatographic MS data |
| chromatogram-MSnExp-method | Extract chromatogram object(s) |
| clean-methods | Clean 'MSnExp', 'Spectrum' or 'Chromatogram' instances |
| combineFeatures | Combines features in an 'MSnSet' object |
| combineSpectra | Combine Spectra |
| combineSpectraMovingWindow | Combine signal from consecutive spectra of LCMS experiments |
| commonFeatureNames | Keep only common feature names |
| compareMSnSets | Compare two MSnSets |
| compareSpectra-methods | Compare Spectra of an 'MSnExp' or 'Spectrum' instances |
| consensusSpectrum | Combine spectra to a consensus spectrum |
| defunct | MSnbase Deprecated and Defunct |
| estimateMzResolution | Estimate the m/z resolution of a spectrum |
| estimateMzScattering | Estimate m/z scattering in consecutive scans |
| estimateNoise-method | Noise Estimation for 'Spectrum' instances |
| extractPrecSpectra-methods | Extracts precursor-specific spectra from an 'MSnExp' object |
| extractSpectraData | Conversion between objects from the Spectra and MSnbase... |
| factorsAsStrings | Converts factors to strings |
| fData-utils | Expand or merge feature variables |
| FeatComp-class | Class '"FeatComp"' |
| featureCV | Calculates coeffivient of variation for features |
| FeaturesOfInterest-class | Features of Interest |
| fillUp | Fills up a vector |
| filterIdentificationDataFrame | Filter out unreliable PSMs. |
| formatRt | Format Retention Time |
| getVariableName | Return a variable name |
| grepEcols | Returns the matching column names of indices. |
| hasSpectraOrChromatograms | Checks if raw data files have any spectra or chromatograms |
| imageNA2 | NA heatmap visualisation for 2 groups |
| impute | Quantitative proteomics data imputation |
| iPQF | iPQF: iTRAQ (and TMT) Protein Quantification based on... |
| isCentroidedFromFile | Get mode from mzML data file |
| iTRAQ4 | iTRAQ 4-plex set |
| itraqdata | Example 'MSnExp' and 'MSnSet' data sets |
| listOf | Tests equality of list elements class |
| makeCamelCase | Convert to camel case by replacing dots by captial letters |
| makeNaData | Create a data with missing values |
| MChromatograms-class | Container for multiple Chromatogram objects |
| meanMzInts | Combine a list of spectra to a single spectrum |
| MIAPE-class | The "MIAPE" Class for Storing Proteomics Experiment... |
| missing-data | Documenting missing data visualisation |
| MSmap-class | Class 'MSmap' |
| MSnbaseOptions | MSnbase options |
| MSnExp-class | The 'MSnExp' Class for MS Data And Meta-Data |
| MSnProcess-class | The "MSnProcess" Class |
| MSnSet-class | The "MSnSet" Class for MS Proteomics Expression Data and... |
| MSnSetList-class | Storing multiple related MSnSets |
| MSpectra | List of Spectrum objects along with annotations |
| mzRident2dfr | Coerce identification data to a 'data.frame' |
| MzTab-class | Parse 'MzTab' files |
| naplot | Overview of missing value |
| navMS | Navigate an 'MSnExp' object |
| nFeatures | How many features in a group? |
| normalise-methods | Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects |
| normToReference | Combine peptides into proteins. |
| npcv | Non-parametric coefficient of variation |
| nQuants | Count the number of quantitfied features. |
| OnDiskMSnExp-class | The 'OnDiskMSnExp' Class for MS Data And Meta-Data |
| pickPeaks-method | Peak Detection for 'MSnExp' or 'Spectrum' instances |
| plot2d-methods | The 'plot2d' method for 'MSnExp' quality assessment |
| plotDensity-methods | The 'plotDensity' method for 'MSnExp' quality assessment |
| plot-methods | Plotting 'MSnExp' and 'Spectrum' object(s) |
| plotMzDelta-methods | The delta m/z plot |
| plotNA-methods | Exploring missing data in 'MSnSet' instances |
| plotSpectrumSpectrum-methods | Plotting a 'Spectrum' vs another 'Spectrum' object. |
| precSelection | Number of precursor selection events |
| ProcessingStep-class | Simple processing step class |
| pSet-class | Class to Contain Raw Mass-Spectrometry Assays and... |
| purityCorrect-methods | Performs reporter ions purity correction |
| quantify-methods | Quantifies 'MSnExp' and 'Spectrum' objects |
| readMgfData | Import mgf files as 'MSnExp' instances. |
| readMSData | Imports mass-spectrometry raw data files as 'MSnExp'... |
| readMSnSet | 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-data.frame-method | Reduce a data.frame |
| removeNoId-methods | Removes non-identified features |
| removePeaks-methods | Removes low intensity peaks |
| removeReporters-methods | Removes reporter ion tag peaks |
| ReporterIons-class | The "ReporterIons" Class |
| selectFeatureData | Select feature variables of interest |
| smooth-methods | Smooths 'MSnExp' or 'Spectrum' instances |
| Spectrum1-class | The "Spectrum1" Class for MS1 Spectra |
| Spectrum2-class | The "Spectrum2" Class for MSn Spectra |
| Spectrum-class | The "Spectrum" Class |
| TMT6 | TMT 6/10-plex sets |
| trimMz-methods | Trims 'MSnExp' or 'Spectrum' instances |
| updateObject-methods | Update MSnbase objects |
| writeMgfData-methods | Write an experiment or spectrum to an mgf file |
| writeMSData | Write MS data to mzML or mzXML files |
| writeMzTabData | Export an MzTab object as mzTab file. |
