Protein Mass Spectra Processing

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Documentation for package ‘msProcess’ version 1.0.4

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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
argNames Display the Argument List of a Function
Arith,numeric,proteins-method Class Representing a Protein Mixture or Sample
Arith,proteins,integer-method Class Representing a Protein Mixture or Sample
Arith,proteins,missing-method Class Representing a Protein Mixture or Sample
Arith,proteins,proteins-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,numeric,proteins-method Class Representing a Protein Mixture or Sample
Compare,proteins,integer-method Class Representing a Protein Mixture or Sample
Compare,proteins,proteins-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,ANY,proteins-method Class Representing a Protein Mixture or Sample
Logic,proteins,ANY-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,proteins-method Class Representing a Protein Mixture or Sample
Math2,proteins-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,proteins,missing-method Class Representing a Protein Mixture or Sample
plot,spectrum,missing-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,spectrometer,calibrants-method Class Representing a Mass Spectrometer
run,spectrometer,proteins-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,proteins-method Class Representing a Protein Mixture or Sample
show,setting-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,proteins-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 --

[,msList-method S3 Class Representing a List of Spectra with Possibly Different m/z Values
[,msSet-method S3 Class Representing a Set of Spectra with Common m/z Values
[,proteins-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
[<-,proteins,ANY,ANY,ANY-method Class Representing a Protein Mixture or Sample
[<-,proteins,ANY,ANY,proteins-method Class Representing a Protein Mixture or Sample