apply                   S3 generic apply method for msSet Class
argNames                Display the Argument List of a Function
assignEvent             Update a Previously Thrown History Event with
                        New Information
calibrants              Class Representing a Set of Calibrants
calibrator              Class Representing the Calibrator of a Mass
                        Spectrometer
catchEvent              Catch a History Event that has been Thrown
cypherGenXML2Bin        Convert Cyphergen XML files into binary files
eventHistory            Event History Creation
existHistory            Verify Existence of an Embedded History Object
getHistory              Extract an Event History from an Arbitrary
                        Object
importBin2Sqlite        Import binary file into SQL
importXMLDir            Import a directory of cyphergenXML files into
                        SQLite
ion.focus.delay         Simulating Linear MALDI-TOF with Ion Focus
                        Delay
isProcessRecorded       Verifies the Existence of a Recorded Process in
                        a Thrown Event
matchObject             Search for an Object Name Matching a Character
                        String on the Data Directory Search List
msAlign                 Peak Alignment
msAssign                Utility functions for maintaining pipeline
                        processing histories
msCalibrate             Constructor Function for Objects of Class
                        msCalibrate
msCharge                Charge Detection
msDenoise               Mother Function for Mass Spectra Denoising
msDenoiseMRD            Denoising a Mass Spectrum via Partial Summation
                        of an MRD
msDenoiseSmooth         Denoising Mass Spectra via Smoothing
msDenoiseWavelet        Denoising a Mass Spectrum via Wavelet Shrinkage
msDenoiseWaveletThreshold
                        Wavelet Shrinkage Threshold Test
msDetrend               Baseline Correction
msExtrema               Find both Local Maxima and Local Minima
msHelp                  Open msProcess Help Files in S-PLUS
msImport                Mass Spectra Data Import
msImportCiphergenXML    Import Mass Spectrometry Data from a Ciphergen
                        XML File
msLaunchExample         Open msProcess Example/Demo Files in S-PLUS
msList                  S3 Class Representing a List of Spectra with
                        Possibly Different m/z Values
msLogic                 Processing Logic
msNoise                 Local Noise Estimation
msNormalize             Mother Function for Intensity Normalization
msNormalizeSNV          Standard Normal Variate Intensity Normalization
msNormalizeTIC          Intensity Normalization Using Total Ion Current
msObjects               Finding msSet Object Names
msPeak                  Mother Function for Peak Detection
msPeakCWT               Peak Detection via the Continuous Wavelet
                        Transform
msPeakInfo              Peak Detection Constructor Function
msPeakMRD               Peak Detection via Multiresolution
                        Decomposition
msPeakSearch            Peak Detection via Elevated Intensity
msPeakSimple            Peak Detection via Local Maxima
msPlot                  General Plotting Utility
msPrepare               Convert an msList Object to an msSet Object
msProcess-package       Protein Mass Spectra Processing
msQualify               Quality Assessment of Mass Spectra Data
msQuantify              Mother Function for Peak Quantification
msQuantifyCount         Count of Spectral Peaks Associated with a Peak
                        Class
msQuantifyIntensity     Spectral Peak Intensities Associated with a
                        Peak Class
msSet                   S3 Class Representing a Set of Spectra with
                        Common m/z Values
msSmoothApprox          Piecewise Linear Baseline Estimation
msSmoothKsmooth         Fit a Smooth Curve Using Kernel Smoothers
msSmoothLoess           Fit a Smooth Curve Using Loess
msSmoothMRD             Baseline Estimation via Partial Summation of an
                        MRD
msSmoothMean            Fit a Smooth Curve Using Moving Average
msSmoothMonotone        Monotonic Baseline Estimation
msSmoothSpline          Fit a Smooth Curve Using Cubic Spline
msSmoothSupsmu          Fit a Smooth Curve Using Super Smoother
msVisual                Determining What Can Be Visualized
princomp2               Principal Component Analysis for Wide Data
proteins                Class Representing a Protein Mixture or Sample
qclist                  Mass Spectra from a Breast Cancer Quality
                        Control Sample
qcset                   Mass Spectra from a Breast Cancer Quality
                        Control Sample
readBinMatrix           Read a binary file containing dimension
                        information
rescale                 Rescale a Vector or a Matrix to the Specified
                        Limits
setting                 Class Representing the Setting of a Mass
                        Spectrometer
spectrometer            Class Representing a Mass Spectrometer
spectrum                Class Representing a Spectrum
throwEvent              Throw a History Event to a Specified Frame
writeBinBlocks          Write a series of binary files containing data
                        blocks
zeroCross               Find the Zero Crossing of a Time Series
