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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 |
| 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,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 |
| binblocks2SQLite | Import binary file into SQL |
| 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 |
| eventHistory | Event History Creation |
| existHistory | Verify Existence of an Embedded History Object |
| formula.msCalibrate | Constructor Function for Objects of Class msCalibrate |
| getHistory | Extract an Event History from an Arbitrary Object |
| 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 |
| Logic,ANY,proteins-method | Class Representing a Protein Mixture or Sample |
| Logic,proteins,ANY-method | Class Representing a Protein Mixture or Sample |
| 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 |
| 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 |
| 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 |
| run | Class Representing a Mass Spectrometer |
| run,spectrometer,calibrants-method | Class Representing a Mass Spectrometer |
| run,spectrometer,proteins-method | Class Representing a Mass Spectrometer |
| 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 |
| 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 |
| [,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 |