# Protein Mass Spectra Processing

## Documentation for package ‘msProcess’ version 1.0.6

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Code demos. Use demo() to run them.

## Help Pages

A B C E F G I L M P Q R S T W Z misc

msProcess-package | Protein Mass Spectra Processing

## -- A --

apply | S3 generic apply method for msSet Class
apply.default | S3 generic apply method for msSet Class
apply.msSet | S3 generic apply method for msSet Class
argNames | Display the Argument List of a Function
Arith-method | Class Representing a Protein Mixture or Sample
assignEvent | Update a Previously Thrown History Event with New Information

## -- B --

binblocks2SQLite | Import binary file into SQL

## -- C --

calibrants | Class Representing a Set of Calibrants
calibrants-class | Class Representing a Set of Calibrants
calibrator | Class Representing the Calibrator of a Mass Spectrometer
calibrator-class | Class Representing the Calibrator of a Mass Spectrometer
catchEvent | Catch a History Event that has been Thrown
coef.msCalibrate | Constructor Function for Objects of Class msCalibrate
Compare-method | Class Representing a Protein Mixture or Sample
cypherGenXML2Bin | Convert Cyphergen XML files into binary files
cypherGenXMList2BinBlocks | Convert Cyphergen XML files into binary files

## -- E --

eventHistory | Event History Creation
existHistory | Verify Existence of an Embedded History Object

## -- F --

formula.msCalibrate | Constructor Function for Objects of Class msCalibrate

## -- G --

getHistory | Extract an Event History from an Arbitrary Object

## -- I --

image.msSet | S3 Class Representing a Set of Spectra with Common m/z Values
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

## -- L --

Logic-method | Class Representing a Protein Mixture or Sample

## -- M --

matchObject | Search for an Object Name Matching a Character String on the Data Directory Search List
Math-method | Class Representing a Protein Mixture or Sample
Math2-method | Class Representing a Protein Mixture or Sample
merge.msList | S3 Class Representing a List of Spectra with Possibly Different m/z Values
msAlign | Peak Alignment
msAlignCluster | Peak Alignment
msAlignGap | Peak Alignment
msAlignMRD | Peak Alignment
msAlignVote | 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
msExists | Utility functions for maintaining pipeline processing histories
msExtrema | Find both Local Maxima and Local Minima
msGet | Utility functions for maintaining pipeline processing histories
msGlobalEnv | Utility functions for maintaining pipeline processing histories
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
msList-class | S3 Class Representing a List of Spectra with Possibly Different m/z Values
msLogic | Processing Logic
msNewEnv | Utility functions for maintaining pipeline processing histories
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 | 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
msRemove | Utility functions for maintaining pipeline processing histories
msSet | S3 Class Representing a Set of Spectra with Common m/z Values
msSet-class | 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
msSmoothMean | Fit a Smooth Curve Using Moving Average
msSmoothMonotone | Monotonic Baseline Estimation
msSmoothMRD | Baseline Estimation via Partial Summation of an MRD
msSmoothSpline | Fit a Smooth Curve Using Cubic Spline
msSmoothSupsmu | Fit a Smooth Curve Using Super Smoother
msVisual | Determining What Can Be Visualized

## -- P --

plot-method | Class Representing a Protein Mixture or Sample
plot-method | Class Representing a Spectrum
plot.msCalibrate | Constructor Function for Objects of Class msCalibrate
plot.msDenoiseWaveletThreshold | Wavelet Shrinkage Threshold Test
plot.msList | S3 Class Representing a List of Spectra with Possibly Different m/z Values
plot.msSet | S3 Class Representing a Set of Spectra with Common m/z Values
predict.msCalibrate | Constructor Function for Objects of Class msCalibrate
predict.msQualify | Quality Assessment of Mass Spectra Data
princomp2 | Principal Component Analysis for Wide Data
print.eventHistory | Event History Creation
print.msCalibrate | Constructor Function for Objects of Class msCalibrate
print.msDenoiseWaveletThreshold | Wavelet Shrinkage Threshold Test
print.msList | S3 Class Representing a List of Spectra with Possibly Different m/z Values
print.msSet | S3 Class Representing a Set of Spectra with Common m/z Values
print.summary.msList | S3 Class Representing a List of Spectra with Possibly Different m/z Values
print.summary.msSet | S3 Class Representing a Set of Spectra with Common m/z Values
proteins | Class Representing a Protein Mixture or Sample
proteins-class | Class Representing a Protein Mixture or Sample

## -- Q --

qclist | Mass Spectra from a Breast Cancer Quality Control Sample
qcset | Mass Spectra from a Breast Cancer Quality Control Sample

## -- R --

readBinMatrix | Read a binary file containing dimension information
rescale | Rescale a Vector or a Matrix to the Specified Limits
run | Class Representing a Mass Spectrometer
run-method | Class Representing a Mass Spectrometer

## -- S --

setting | Class Representing the Setting of a Mass Spectrometer
setting-class | Class Representing the Setting of a Mass Spectrometer
show-method | Class Representing a Protein Mixture or Sample
show-method | Class Representing the Setting of a Mass Spectrometer
spectrometer | Class Representing a Mass Spectrometer
spectrometer-class | Class Representing a Mass Spectrometer
spectrum | Class Representing a Spectrum
spectrum-class | Class Representing a Spectrum
Summary-method | Class Representing a Protein Mixture or Sample
summary.msList | S3 Class Representing a List of Spectra with Possibly Different m/z Values
summary.msList-class | S3 Class Representing a List of Spectra with Possibly Different m/z Values
summary.msSet | S3 Class Representing a Set of Spectra with Common m/z Values

## -- T --

throwEvent | Throw a History Event to a Specified Frame

## -- W --

writeBinBlocks | Write a series of binary files containing data blocks

## -- Z --

zeroCross | Find the Zero Crossing of a Time Series

## -- misc --

[-method | S3 Class Representing a List of Spectra with Possibly Different m/z Values
[-method | S3 Class Representing a Set of Spectra with Common m/z Values
[-method | Class Representing a Protein Mixture or Sample
[.eventHistory | Event History Creation
[.msList | S3 Class Representing a List of Spectra with Possibly Different m/z Values
[.msSet | S3 Class Representing a Set of Spectra with Common m/z Values
[<--method | Class Representing a Protein Mixture or Sample