Chromatogram            Representation of chromatographic MS data
FeatComp-class          Class '"FeatComp"'
FeaturesOfInterest-class
                        Features of Interest
MChromatograms          Container for multiple Chromatogram objects
MIAPE-class             The "MIAPE" Class for Storing Proteomics
                        Experiment Information
MSmap-class             Class 'MSmap'
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
MSnbaseOptions          MSnbase options
MSpectra                List of Spectrum objects along with annotations
MzTab-class             Parse 'MzTab' files
OnDiskMSnExp-class      The 'OnDiskMSnExp' Class for MS Data And
                        Meta-Data
ProcessingStep-class    Simple processing step class
ReporterIons-class      The "ReporterIons" Class
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
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,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
featureCV               Calculates coeffivient of variation for
                        features
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
iPQF                    iPQF: iTRAQ (and TMT) Protein Quantification
                        based on Features
iTRAQ4                  iTRAQ 4-plex set
imageNA2                NA heatmap visualisation for 2 groups
impute,MSnSet-method    Quantitative proteomics data imputation
isCentroidedFromFile    Get mode from mzML data file
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
meanMzInts              Combine a list of spectra to a single spectrum
missing-data            Documenting missing data visualisation
nFeatures               How many features in a group?
nQuants                 Count the number of quantitfied features.
naplot                  Overview of missing value
normToReference         Combine peptides into proteins.
normalise-methods       Normalisation of 'MSnExp', 'MSnSet' and
                        'Spectrum' objects
npcv                    Non-parametric coefficient of variation
pSet-class              Class to Contain Raw Mass-Spectrometry Assays
                        and Experimental Metadata
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
purityCorrect-methods   Performs reporter ions purity correction
quantify-methods        Quantifies 'MSnExp' and 'Spectrum' objects
readMSData              Imports mass-spectrometry raw data files as
                        'MSnExp' instances.
readMSnSet              Read 'MSnSet'
readMgfData             Import mgf files as 'MSnExp' instances.
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
selectFeatureData       Select feature variables of interest
smooth-methods          Smooths 'MSnExp' or 'Spectrum' instances
trimMz-methods          Trims 'MSnExp' or 'Spectrum' instances
updateObject,MSnExp-method
                        Update MSnbase objects
writeMSData,MSnExp,character-method
                        Write MS data to mzML or mzXML files
writeMgfData-methods    Write an experiment or spectrum to an mgf file
writeMzTabData          Export an MzTab object as mzTab file.
