addIdentificationData-methods
                        Adds Identification Data
aggvar                  Identify aggregation outliers
as                      Coerce identification data to a 'data.frame'
averageMSnSet           Generate an average 'MSnSet'
bin-methods             Bin 'MSnExp' or 'Spectrum' instances
calculateFragments      Calculate ions produced by fragmentation.
Chromatogram            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,MSnExp-method
                        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
estimateMzResolution,MSnExp-method
                        Estimate the m/z resolution of a spectrum
estimateMzScattering    Estimate m/z scattering in consecutive scans
estimateNoise-methods   Noise Estimation for 'Spectrum' instances
expandFeatureVars       Expand or merge feature variables
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
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.
hasSpectra              Checks if raw data files have any spectra or
                        chromatograms
imageNA2                NA heatmap visualisation for 2 groups
impute,MSnSet-method    Quantitative proteomics data imputation
iPQF                    iPQF: iTRAQ (and TMT) Protein Quantification
                        based on Features
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          Container for multiple Chromatogram objects
meanMzInts              Combine a list of spectra to a single spectrum
MIAPE-class             The "MIAPE" Class for Storing Proteomics
                        Experiment Information
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 Meta-Data
MSnSetList-class        Storing multiple related MSnSets
MSpectra                List of Spectrum objects along with annotations
MzTab-class             Parse 'MzTab' files
naplot                  Overview of missing value
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-methods       Peak Detection for 'MSnExp' or 'Spectrum'
                        instances
plot-methods            Plotting 'MSnExp' and 'Spectrum' object(s)
plot.Spectrum.Spectrum
                        Plotting a 'Spectrum' vs another 'Spectrum'
                        object.
plot2d-methods          The 'plot2d' method for 'MSnExp' quality
                        assessment
plotDensity-methods     The 'plotDensity' method for 'MSnExp' quality
                        assessment
plotMzDelta-methods     The delta m/z plot
plotNA-methods          Exploring missing data in 'MSnSet' instances
precSelection           Number of precursor selection events
ProcessingStep-class    Simple processing step class
pSet-class              Class to Contain Raw Mass-Spectrometry Assays
                        and Experimental Metadata
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' instances.
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
Spectrum-class          The "Spectrum" Class
Spectrum1-class         The "Spectrum1" Class for MS1 Spectra
Spectrum2-class         The "Spectrum2" Class for MSn Spectra
TMT6                    TMT 6/10-plex sets
trimMz-methods          Trims 'MSnExp' or 'Spectrum' instances
updateObject,MSnExp-method
                        Update MSnbase objects
writeMgfData-methods    Write an experiment or spectrum to an mgf file
writeMSData,MSnExp,character-method
                        Write MS data to mzML or mzXML files
writeMzTabData          Export an MzTab object as mzTab file.
