FeatComp-class          Class '"FeatComp"'
FeaturesOfInterest-class
                        Features of Interest
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
MSnbase-package         MSnbase: Base Functions and Classes for
                        MS-based Proteomics
MSnbaseOptions          MSnbase options
MzTab-class             Parse 'MzTab' files
NAnnotatedDataFrame-class
                        Class Containing Measured Variables and Their
                        Meta-Data Description for Multiplexed
                        Experiments.
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
averageMSnSet           Generate an average 'MSnSet'
bin-methods             Bin 'MSnExp' or 'Spectrum' instances
calculateFragments      Calculate ions produced by fragmentation.
chromatogram-methods    Plots a chromatogram
clean-methods           Cleans 'MSnExp' or 'Spectrum' instances
combineFeatures         Combines features in an 'MSnSet' object
commonFeatureNames      Keep only common feature names
compareMSnSets          Compare two MSnSets
compareSpectra-methods
                        Compare Spectra of an 'MSnExp' or 'Spectrum'
                        instances
estimateNoise-methods   Noise Estimation for 'Spectrum' instances
exprsToRatios-methods   Calculate all ratio pairs
extractPrecSpectra-methods
                        Extracts precursor-specific spectra from an
                        'MSnExp' object
featureCV               Calculates coeffivient of variation for
                        features
fillUp                  Fills up a vector
formatRt                Format Retention Time
get.amino.acids         Amino acids
get.atomic.mass         Atomic mass.
getVariableName         Return a variable name
grepEcols               Returns the matching column names of indices.
iPQF                    iPQF: iTRAQ (and TMT) Protein Quantification
                        based on Features
iTRAQ4                  iTRAQ 4-plex set
imageNA2                NA heatmap visualisation for 2 groups
impute-methods          Quantitative proteomics data imputation
itraqdata               Example 'MSnExp' and 'MSnSet' data sets
listOf                  Tests equality of list elements class
makeNaData              Create a data with missing values
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
navMS                   Navigate an 'MSnExp' object
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 '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.
readMzTabData           Read an 'mzTab' file
readMzTabData_v0.9      Read an 'mzTab' file
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
writeMgfData-methods    Write an experiment or spectrum to an mgf file
xic-methods             Extracted ion chromatograms
