Quantitative analysis of MALDI-TOF MS data

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Documentation for package ‘MALDIquant’ version 0.5

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MALDIquant-package Quantitative analysis of MALDI-TOF MS data
.estimateBaselineConvexHull Estimates the baseline by a Convex Hull.
.estimateBaselineMedian Estimates the baseline by moving estimators.
.estimateBaselineSnip Estimates the baseline by SNIP algorithm.
AbstractMassObject-class Class "AbstractMassObject"
as.matrix-method Class "AbstractMassObject"
calibrate Calibrates MassObject objects.
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.
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.
findEmptyMassObjects Finds or removes empty AbstractMassObject objects in a list.
findLocalMaxima Find local maxima in a MassSpectrum object.
findLocalMaxima-method Find local maxima in a MassSpectrum object.
imputeMass Imputes missing mass values to a MassSpectrum object.
imputeMass-method Imputes missing mass values to a MassSpectrum object.
intensity Class "AbstractMassObject"
intensity-method Class "AbstractMassObject"
intensity<- Class "AbstractMassObject"
intensity<--method Class "AbstractMassObject"
intensityMatrix Converts a list MassObject objects into a matrix.
isEmpty Class "AbstractMassObject"
isEmpty-method Class "AbstractMassObject"
isMassObjectList Tests a list of AbstractMassObject objects.
isMassPeaksList Tests a list of AbstractMassObject objects.
isMassSpectrumList Tests a list of AbstractMassObject objects.
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 MALDI-TOF MS data
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"
metaData Class "AbstractMassObject"
metaData-method Class "AbstractMassObject"
metaData<- Class "AbstractMassObject"
metaData<--method Class "AbstractMassObject"
pA1 Example Mass Spectra (extracted peaks)
plot-method Plots an AbstractMassObject object.
points-method Class "AbstractMassObject"
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.
sA1 Example Mass Spectra (raw)
transformIntensity Transforms Intensities of an AbstractMassObject object.
transformIntensity-method Transforms Intensities of an AbstractMassObject object.