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 |
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 |