Man pages for zeehio/msProcess
Protein Mass Spectra Processing
| 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 |
| dbcypherGenXML2Bin | Convert Cyphergen XML files into binary files |
| dbimportBin2Sqlite | Import binary file into SQL |
| dbimportXMLDir | Import a directory of cyphergenXML files into SQLite |
| dbreadBinDim | Read a binary file containing dimension information |
| dbwriteBinDim | Write a series of binary files containing data blocks |
| eventHistory | Event History Creation |
| existHistory | Verify Existence of an Embedded History Object |
| getHistory | Extract an Event History from an Arbitrary Object |
| ion.focus.delay | Simulating Linear MALDI-TOF with Ion Focus Delay |
| isProcessRecorded | Verifies the Existence of a Recorded Process in a Thrown... |
| matchObject | Search for an Object Name Matching a Character String on the... |
| msAlign | Peak Alignment |
| msAssign | Utility functions for maintaining pipeline processing... |
| 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... |
| 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 |
| 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 |
| 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 |
| 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 |
| zeroCross | Find the Zero Crossing of a Time Series |
