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" |
match.closest |
Relaxed Value Matching |
mergeMassPeaks |
Merges 'MassPeaks' objects. |
metaData |
Class "AbstractMassObject" |
metaData-method |
Class "AbstractMassObject" |
metaData<- |
Class "AbstractMassObject" |
metaData<--method |
Class "AbstractMassObject" |
monoisotopicPeaks |
Finds monoisotopic peaks in a MassPeaks object. |
monoisotopicPeaks-method |
Finds monoisotopic peaks in a MassPeaks object. |
msiSlices |
Turn a list of AbstractMassObjects into a mass spectrometry imaging slice. |
mz |
Class "AbstractMassObject" |
mz-method |
Class "AbstractMassObject" |
mz<- |
Class "AbstractMassObject" |
mz<--method |
Class "AbstractMassObject" |
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" |