Quantitative Analysis of Mass Spectrometry Data

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Documentation for package ‘MALDIquant’ version 1.14

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MALDIquant-package Quantitative Analysis of Mass Spectrometry Data
AbstractMassObject-class Class "AbstractMassObject"
alignSpectra Align MassSpectrum objects.
as.matrix-method Class "AbstractMassObject"
averageMassSpectra Averages 'MassSpectrum' objects.
binPeaks Align Peaks into discrete bins.
calibrateIntensity Calibrates intensities of a MassSpectrum object.
calibrateIntensity-method Calibrates intensities of a MassSpectrum object.
coordinates Class "AbstractMassObject"
coordinates-method Class "AbstractMassObject"
coordinates<- Class "AbstractMassObject"
coordinates<--method Class "AbstractMassObject"
createMassPeaks Creates a MassPeaks object.
createMassSpectrum Creates a MassSpectrum object.
detectPeaks Detects peaks in a MassSpectrum object.
detectPeaks-method Detects peaks in a MassSpectrum object.
determineWarpingFunctions Determine warping functions of MassPeaks objects.
estimateBaseline Estimates the baseline of a MassSpectrum object.
estimateBaseline-method Estimates the baseline of a MassSpectrum object.
estimateNoise Estimates the noise of a MassSpectrum object.
estimateNoise-method Estimates the noise of a MassSpectrum object.
fiedler2009subset Example Mass Spectra (raw)
filterPeaks Removes less frequent peaks.
findEmptyMassObjects Finds or removes empty AbstractMassObject objects in a list.
intensity Class "AbstractMassObject"
intensity-method Class "AbstractMassObject"
intensity<- Class "AbstractMassObject"
intensity<--method Class "AbstractMassObject"
intensityMatrix Converts a list of MassPeaks objects into a matrix.
isEmpty Class "AbstractMassObject"
isEmpty-method Class "AbstractMassObject"
isMassPeaks Tests for MassSpectrum or MassPeaks object.
isMassPeaksList Tests a list of MassSpectrum or MassPeaks objects.
isMassSpectrum Tests for MassSpectrum or MassPeaks object.
isMassSpectrumList Tests a list of MassSpectrum or MassPeaks objects.
isRegular Class "MassSpectrum"
isRegular-method Class "MassSpectrum"
labelPeaks Draws peak labels to plot.
labelPeaks-method Draws peak labels to plot.
length-method Class "AbstractMassObject"
lines-method Class "AbstractMassObject"
MALDIquant Quantitative Analysis of Mass Spectrometry Data
MALDIquant-parallel Parallel Support in Package 'MALDIquant'
mass Class "AbstractMassObject"
mass-method Class "AbstractMassObject"
mass<- Class "AbstractMassObject"
mass<--method Class "AbstractMassObject"
MassPeaks Class "MassPeaks"
MassPeaks-class Class "MassPeaks"
MassSpectrum Class "MassSpectrum"
MassSpectrum-class Class "MassSpectrum"
mergeMassPeaks Merges 'MassPeaks' objects.
metaData Class "AbstractMassObject"
metaData-method Class "AbstractMassObject"
metaData<- Class "AbstractMassObject"
metaData<--method Class "AbstractMassObject"
msiSlices Turn a list of AbstractMassObjects into a mass spectrometry imaging slice.
plot-method Plots an AbstractMassObject object.
plotMsiSlice Plots a Mass Spectrometry Imaging dataset.
plotMsiSlice-method Plots a Mass Spectrometry Imaging dataset.
points-method Class "AbstractMassObject"
referencePeaks Creates a reference 'MassPeaks' object.
removeBaseline Removes the baseline of a MassSpectrum object.
removeBaseline-method Removes the baseline of a MassSpectrum object.
removeEmptyMassObjects Finds or removes empty AbstractMassObject objects in a list.
smoothIntensity Smoothes intensities of a MassSpectrum object.
smoothIntensity-method Smoothes intensities of a MassSpectrum object.
snr Class "MassPeaks"
snr-method Class "MassPeaks"
totalIonCurrent Class "MassSpectrum"
totalIonCurrent-method Class "MassSpectrum"
transformIntensity Transforms intensities of an AbstractMassObject object.
transformIntensity-method Transforms intensities of an AbstractMassObject object.
trim Trim an AbstractMassObject object.
trim-method Trim an AbstractMassObject object.
warpMassPeaks Run warping functions on AbstractMassObject objects.
warpMassSpectra Run warping functions on AbstractMassObject objects.
[-method Class "AbstractMassObject"