MALDIquant
Quantitative Analysis of Mass Spectrometry Data

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Functions
203
Source code
148
Man pages
36
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MALDIquant: Quantitative Analysis of Mass Spectrometry Data
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API

API for MALDIquant
Quantitative Analysis of Mass Spectrometry Data

Global functions
. Man page
.F Source code
.P Source code
.Psum Source code
.as.binary.matrix Source code
.as.matrix.MassObjectList Source code
.as.occurrence.list.MassObjectList Source code
.averageMassSpectra Source code
.binPeaks Source code
.calculateLabelPositions Source code
.calibrateIntensitySimple Source code
.calibrateProbabilisticQuotientNormalization Source code
.colCors Source code
.colMaxs Source code
.colMedians Source code
.deprecated Source code
.deprecatedArgument Source code
.deprecatedFunction Source code
.dilation Source code
.doByLabels Source code
.erosion Source code
.estimateBaseline Source code
.estimateBaselineConvexHull Source code
.estimateBaselineMedian Source code
.estimateBaselineSnip Source code
.estimateBaselineTopHat Source code
.estimateNoise Source code
.estimateNoiseMad Source code
.estimateNoiseSuperSmoother Source code
.filter Source code
.grouperRelaxed Source code
.grouperRelaxedHighestAtReference Source code
.grouperStrict Source code
.irregularScore Source code
.isFunctionList Source code
.isMassObject Source code
.isMassObjectList Source code
.lapply Source code
.localMaxima Source code
.mapply Source code
.memoryUsageStr Source code
.mergeMassPeaks Source code
.mergeMetaData Source code
.monoisotopic Source code
.monoisotopicPattern Source code
.movingAverage Source code
.msiSlices Source code
.onAttach Source code
.overlap Source code
.overlaps Source code
.plotMsiSlice Source code
.prepareShowGroupName Source code
.pseudoCluster Source code
.reorder Source code
.reorderRange Source code
.replaceNegativeIntensityValues Source code
.rotate Source code
.savitzkyGolay Source code
.savitzkyGolayCoefficients Source code
.scaleFactor Source code
.scalingFactor Source code
.stopIfNotIsFunctionList Source code
.stopIfNotIsMassObjectList Source code
.stopIfNotIsMassPeaksList Source code
.stopIfNotIsMassSpectrumList Source code
.stopIfNotIsValidHalfWindowSize Source code
.strWH Source code
.testLabelOverlap Source code
.textLabelRects Source code
.unlist Source code
.validAbstractMassObject Source code
.validMassPeaks Source code
.warp Source code
.warpingFunctionCubic Source code
.warpingFunctionLinear Source code
.warpingFunctionLowess Source code
.warpingFunctionQuadratic Source code
.which.closest Source code
.whitelist Source code
AbstractMassObject-class Man page
MALDIquant Man page
MALDIquant-defunct Man page
MALDIquant-deprecated Man page
MALDIquant-package Man page
MALDIquant-parallel Man page
MassPeaks Man page
MassPeaks-class Man page
MassSpectrum Man page
MassSpectrum-class Man page
[,AbstractMassObject,logical,missing-method Man page
[,AbstractMassObject,numeric,missing-method Man page
[,MassPeaks,logical,missing-method Man page
[,MassPeaks,numeric,missing-method Man page
alignSpectra Man page Source code
as.matrix,AbstractMassObject-method Man page
averageMassSpectra Man page Source code
binPeaks Man page Source code
calibrateIntensity Man page
calibrateIntensity,MassSpectrum-method Man page
calibrateIntensity,list-method Man page
coordinates Man page
coordinates,AbstractMassObject-method Man page
coordinates,list-method Man page
coordinates<- Man page
coordinates<-,AbstractMassObject,matrix-method Man page
coordinates<-,AbstractMassObject,numeric-method Man page
coordinates<-,list,matrix-method Man page
createMassPeaks Man page Source code
createMassSpectrum Man page Source code
detectPeaks Man page
detectPeaks,MassSpectrum-method Man page
detectPeaks,list-method Man page
determineWarpingFunctions Man page Source code
estimateBaseline Man page
estimateBaseline,MassSpectrum-method Man page
estimateNoise Man page
estimateNoise,MassSpectrum-method Man page
fiedler2009subset Man page
filterPeaks Man page Source code
findEmptyMassObjects Man page Source code
intensity Man page
intensity,AbstractMassObject-method Man page
intensity<- Man page
intensity<-,AbstractMassObject,numeric-method Man page
intensityMatrix Man page Source code
isEmpty Man page
isEmpty,AbstractMassObject-method Man page
isMassPeaks Man page Source code
isMassPeaksList Man page Source code
isMassSpectrum Man page Source code
isMassSpectrumList Man page Source code
isRegular Man page
isRegular,MassSpectrum-method Man page
labelPeaks Man page
labelPeaks,MassPeaks-method Man page
length,AbstractMassObject-method Man page
lines,AbstractMassObject-method Man page
mass Man page
mass,AbstractMassObject-method Man page
mass<- Man page
mass<-,AbstractMassObject,numeric-method Man page
match.closest Man page Source code
mergeMassPeaks Man page Source code
metaData Man page
metaData,AbstractMassObject-method Man page
metaData<- Man page
metaData<-,AbstractMassObject-method Man page
monoisotopicPeaks Man page
monoisotopicPeaks,MassPeaks-method Man page
monoisotopicPeaks,list-method Man page
msiSlices Man page Source code
mz Man page
mz,AbstractMassObject-method Man page
mz<- Man page
mz<-,AbstractMassObject,numeric-method Man page
plot,AbstractMassObject,missing-method Man page
plot,MassSpectrum,missing-method Man page
plotMsiSlice Man page
plotMsiSlice,array-method Man page
plotMsiSlice,list-method Man page
plotMsiSlice,matrix-method Man page
points,AbstractMassObject-method Man page
referencePeaks Man page Source code
removeBaseline Man page
removeBaseline,MassSpectrum-method Man page
removeBaseline,list-method Man page
removeEmptyMassObjects Man page Source code
smoothIntensity Man page
smoothIntensity,MassSpectrum-method Man page
smoothIntensity,list-method Man page
snr Man page
snr,MassPeaks-method Man page
totalIonCurrent Man page
totalIonCurrent,MassSpectrum-method Man page
transformIntensity Man page
transformIntensity,AbstractMassObject-method Man page
transformIntensity,list-method Man page
trim Man page
trim,AbstractMassObject,numeric-method Man page
trim,list,missing-method Man page
trim,list,numeric-method Man page
warpMassPeaks Man page Source code
warpMassSpectra Man page Source code
MALDIquant documentation built on Sept. 11, 2024, 6:15 p.m.

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