MALDIquant: Quantitative Analysis of Mass Spectrometry Data
Version 1.16.2

A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.

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AuthorSebastian Gibb [aut, cre], Korbinian Strimmer [ths]
Date of publication2017-04-04 15:44:58 UTC
MaintainerSebastian Gibb <mail@sebastiangibb.de>
LicenseGPL (>= 3)
Version1.16.2
URL http://strimmerlab.org/software/maldiquant/ https://github.com/sgibb/MALDIquant/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("MALDIquant")

Man pages

AbstractMassObject-class: Class "AbstractMassObject"
alignSpectra-functions: Align MassSpectrum objects.
averageMassSpectra-functions: Averages 'MassSpectrum' objects.
binPeaks-functions: Align Peaks into discrete bins.
calibrateIntensity-methods: Calibrates intensities of a MassSpectrum object.
createMassPeaks-functions: Creates a MassPeaks object.
createMassSpectrum-functions: Creates a MassSpectrum object.
detectPeaks-methods: Detects peaks in a MassSpectrum object.
determineWarpingFunctions-functions: Determine warping functions of MassPeaks objects.
estimateBaseline-methods: Estimates the baseline of a MassSpectrum object.
estimateNoise-methods: Estimates the noise of a MassSpectrum object.
fiedler2009subset: Example Mass Spectra (raw)
filterPeaks-functions: Removes less frequent peaks.
findEmptyMassObjects-functions: Finds or removes empty AbstractMassObject objects in a list.
intensityMatrix-functions: Converts a list of MassPeaks objects into a matrix.
isMassObject-functions: Tests for MassSpectrum or MassPeaks object.
isMassObjectList-functions: Tests a list of MassSpectrum or MassPeaks objects.
labelPeaks-methods: Draws peak labels to plot.
MALDIquant-defunct: Removed Functions/Methods in Package 'MALDIquant'
MALDIquant-deprecated: Deprecated Functions/Methods in Package 'MALDIquant'
MALDIquant-package: Quantitative Analysis of Mass Spectrometry Data
MALDIquant-parallel: Parallel Support in Package 'MALDIquant'
MassPeaks-class: Class "MassPeaks"
MassSpectrum-class: Class "MassSpectrum"
match.closest: Relaxed Value Matching
mergeMassPeaks-functions: Merges 'MassPeaks' objects.
monoisotopicPeaks-methods: Finds monoisotopic peaks in a MassPeaks object.
msiSlices-functions: Turn a list of AbstractMassObjects into a mass spectrometry...
plot-methods: Plots an AbstractMassObject object.
plotMsiSlice-methods: Plots a Mass Spectrometry Imaging dataset.
referencePeaks-functions: Creates a reference 'MassPeaks' object.
removeBaseline-methods: Removes the baseline of a MassSpectrum object.
smoothIntensity-methods: Smoothes intensities of a MassSpectrum object.
transformIntensity-methods: Transforms intensities of an AbstractMassObject object.
trim-methods: Trim an AbstractMassObject object.
warp-functions: Run warping functions on AbstractMassObject objects.

Functions

. Man page
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
P Source code
Psum Source code
[,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
array2matrix Source code
as.binary.matrix Source code
as.matrix,AbstractMassObject-method Man page
as.matrix.MassObjectList Source code
averageMassSpectra Man page Source code Source code
binPeaks Man page Source code Source code
calculateLabelPositions Source code
calibrateIntensity Man page
calibrateIntensity,MassSpectrum-method Man page
calibrateIntensity,list-method Man page
calibrateIntensitySimple Source code
calibrateProbabilisticQuotientNormalization Source code
colCors Source code
colMaxs Source code
colMedians Source code
colorMatrix Source code
combineColorMatrices Source code
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
deprecated Source code
deprecatedArgument Source code
deprecatedFunction Source code
detectPeaks Man page
detectPeaks,MassSpectrum-method Man page
detectPeaks,list-method Man page
determineWarpingFunctions Man page Source code
dilation Source code
doByLabels Source code
erosion Source code
estimateBaseline Man page Source code
estimateBaseline,MassSpectrum-method Man page
estimateBaselineConvexHull Source code
estimateBaselineMedian Source code
estimateBaselineSnip Source code
estimateBaselineTopHat Source code
estimateNoise Man page Source code
estimateNoise,MassSpectrum-method Man page
estimateNoiseMad Source code
estimateNoiseSuperSmoother Source code
fiedler2009subset Man page
filter Source code
filterPeaks Man page Source code
findEmptyMassObjects Man page Source code
grouperRelaxed Source code
grouperRelaxedHighestAtReference Source code
grouperStrict 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
lapply Source code
length,AbstractMassObject-method Man page
lines,AbstractMassObject-method Man page
localMaxima Source code
mapply Source code
mass Man page
mass,AbstractMassObject-method Man page
mass<- Man page
mass<-,AbstractMassObject,numeric-method Man page
match.closest Man page Source code
memoryUsageStr Source code
mergeMassPeaks Man page Source code Source code
mergeMetaData Source code
metaData Man page
metaData,AbstractMassObject-method Man page
metaData<- Man page
metaData<-,AbstractMassObject-method Man page
monoisotopic Source code
monoisotopicPattern Source code
monoisotopicPeaks Man page
monoisotopicPeaks,MassPeaks-method Man page
monoisotopicPeaks,list-method Man page
movingAverage Source code
msiLegend Source code
msiSlices Man page Source code Source code
mz Man page
mz,AbstractMassObject-method Man page
mz<- Man page
mz<-,AbstractMassObject,numeric-method Man page
onAttach Source code
overlap Source code
overlaps Source code
plot,AbstractMassObject,missing-method Man page
plot,MassSpectrum,missing-method Man page
plotMsiSlice Man page Source code
plotMsiSlice,array-method Man page
plotMsiSlice,list-method Man page
plotMsiSlice,matrix-method Man page
points,AbstractMassObject-method Man page
prepareShowGroupName Source code
pseudoCluster Source code
rasterSlice Source code
referencePeaks Man page Source code
removeBaseline Man page
removeBaseline,MassSpectrum-method Man page
removeBaseline,list-method Man page
removeEmptyMassObjects Man page Source code
reorderRange Source code
replaceNegativeIntensityValues Source code
rgb Source code
rotate Source code
rregularScore Source code
sFunctionList Source code
sMassObject Source code
sMassObjectList Source code
savitzkyGolay Source code
savitzkyGolayCoefficients Source code
scaleFactor Source code
scalingFactor Source code
smoothIntensity Man page
smoothIntensity,MassSpectrum-method Man page
smoothIntensity,list-method Man page
snr Man page
snr,MassPeaks-method Man page
stopIfNotIsFunctionList Source code
stopIfNotIsMassObjectList Source code
stopIfNotIsMassPeaksList Source code
stopIfNotIsMassSpectrumList Source code
stopIfNotIsValidHalfWindowSize Source code
strWH Source code
testLabelOverlap Source code
textLabelRects Source code
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
unlist Source code
validAbstractMassObject Source code
validMassPeaks Source code
warp Source code
warpMassPeaks Man page Source code
warpMassSpectra Man page Source code
warpingFunctionCubic Source code
warpingFunctionLinear Source code
warpingFunctionLowess Source code
warpingFunctionQuadratic Source code
which.closest Source code
whitelist Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/MALDIquant-intro.R
inst/doc/MALDIquant-intro.Rnw
inst/doc/MALDIquant-intro.pdf
tests
tests/testthat.R
tests/testthat
tests/testthat/test_monoisotopicPeaks-methods.R
tests/testthat/test_irregular-functions.R
tests/testthat/test_msiSlices-functions.R
tests/testthat/test_snr-methods.R
tests/testthat/test_deprecated-functions.R
tests/testthat/test_coordinates-methods.R
tests/testthat/test_transformIntensity-methods.R
tests/testthat/test_removeBaseline-methods.R
tests/testthat/test_detectPeaks-methods.R
tests/testthat/test_referencePeaks-functions.R
tests/testthat/test_grouper-functions.R
tests/testthat/test_determineWarpingFunctions-functions.R
tests/testthat/test_isMassObject-functions.R
tests/testthat/test_estimateNoise-methods.R
tests/testthat/test_valid-functions.R
tests/testthat/test_totalIonCurrent-methods.R
tests/testthat/test_averageMassSpectra-functions.R
tests/testthat/test_isMassObjectList-functions.R
tests/testthat/test_filterPeaks-functions.R
tests/testthat/test_plotMsiSlice-functions.R
tests/testthat/test_intensity-methods.R
tests/testthat/test_constructor-functions.R
tests/testthat/test_findLocalMaximaLogical-methods.R
tests/testthat/test_colMedians-functions.R
tests/testthat/test_metaData-methods.R
tests/testthat/test_calculateLabelPositions-functions.R
tests/testthat/test_match.closest-functions.R
tests/testthat/test_approxfun-methods.R
tests/testthat/test_binPeaks-functions.R
tests/testthat/test_as.matrix-functions.R
tests/testthat/test_mass-methods.R
tests/testthat/test_smoothingFilters-functions.R
tests/testthat/test_as-methods.R
tests/testthat/test_alignSpectra-functions.R
tests/testthat/test_doByLabel-functions.R
tests/testthat/test_unlist-functions.R
tests/testthat/test_calibrateIntensity-methods.R
tests/testthat/test_isEmpty-methods.R
tests/testthat/test_labelPeaks-methods.R
tests/testthat/test_as.matrix-methods.R
tests/testthat/test_isRegular-methods.R
tests/testthat/test_plotMsiSlice-methods.R
tests/testthat/test_estimateBaseline-methods.R
tests/testthat/test_subset-methods.R
tests/testthat/test_findEmptyMassObjects-functions.R
tests/testthat/test_length-methods.R
tests/testthat/test_morphologicalFilter-functions.R
tests/testthat/test_merge-functions.R
tests/testthat/test_localMaxima-functions.R
tests/testthat/test_intensityMatrix-functions.R
tests/testthat/test_mz-methods.R
tests/testthat/test_warpingFunctions-functions.R
tests/testthat/test_trim-methods.R
tests/testthat/test_monoisotopic-functions.R
tests/testthat/test_removeEmptyMassObjects-functions.R
tests/testthat/test_range-functions.R
tests/testthat/test_show-methods.R
tests/testthat/test_smoothIntensity-methods.R
tests/testthat/test_warp-functions.R
tests/testthat/test_mapply-functions.R
tests/testthat/test_replaceNegativeIntensityValues.R
src
src/lowerConvexHull.c
src/morphologicalFilters.c
src/snip.c
src/MALDIquant.h
src/colMedians.c
src/init.c
src/localMaxima.c
NAMESPACE
demo
demo/peaks.R
demo/00Index
demo/workflow.R
demo/warping.R
demo/baseline.R
demo/MALDIquant.R
NEWS
data
data/fiedler2009subset.RData
R
R/calibrateIntensity-functions.R
R/AllClasses.R
R/AllGenerics.R
R/mass-methods.R
R/localMaxima-functions.R
R/Deprecated.R
R/msiSlices-functions.R
R/mz-methods.R
R/colMedians-functions.R
R/mapply-functions.R
R/show-methods.R
R/isValidHalfWindowSize-functions.R
R/filterPeaks-functions.R
R/as.matrix-functions.R
R/estimateNoise-methods.R
R/lines-methods.R
R/intensityMatrix-functions.R
R/warpingFunction-functions.R
R/irregular-functions.R
R/onAttach.R
R/as.matrix-methods.R
R/grouper-functions.R
R/constructor-functions.R
R/isEmpty-methods.R
R/isMassObjectList-functions.R
R/estimateBaseline-methods.R
R/doByLabels-functions.R
R/monoisotopicPeaks-methods.R
R/averageMassSpectra-functions.R
R/deprecated-functions.R
R/merge-functions.R
R/determineWarpingFunctions-functions.R
R/coordinates-methods.R
R/valid-methods.R
R/smoothingFilters-functions.R
R/plotMsiSlice-functions.R
R/removeBaseline-methods.R
R/intensity-methods.R
R/plot-methods.R
R/monoisotopic-functions.R
R/match.closest-functions.R
R/binPeaks-functions.R
R/isMassObject-functions.R
R/unlist-functions.R
R/totalIonCurrent-methods.R
R/morphologicalFilter-functions.R
R/trim-methods.R
R/lapply-functions.R
R/calibrateIntensity-methods.R
R/show-functions.R
R/length-methods.R
R/findEmptyMassObjects-functions.R
R/estimateBaseline-functions.R
R/removeEmptyMassObjects-functions.R
R/findLocalMaxima-methods.R
R/range-functions.R
R/snr-methods.R
R/calculateLabelPositions-functions.R
R/replaceNegativeIntensityValues-functions.R
R/transformIntensity-methods.R
R/alignSpectra-functions.R
R/subset-methods.R
R/detectPeaks-methods.R
R/approxfun-methods.R
R/smoothIntensity-methods.R
R/memoryUsage-functions.R
R/warp-functions.R
R/plotMsiSlice-methods.R
R/labelPeaks-methods.R
R/referencePeaks-functions.R
R/as-methods.R
R/isFunctionList-functions.R
R/isRegular-methods.R
R/estimateNoise-functions.R
R/points-methods.R
R/metaData-methods.R
vignettes
vignettes/bibliography.bib
vignettes/MALDIquant-intro.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/determineWarpingFunctions-functions.Rd
man/findEmptyMassObjects-functions.Rd
man/estimateNoise-methods.Rd
man/trim-methods.Rd
man/estimateBaseline-methods.Rd
man/isMassObject-functions.Rd
man/createMassPeaks-functions.Rd
man/plot-methods.Rd
man/MALDIquant-defunct.Rd
man/msiSlices-functions.Rd
man/warp-functions.Rd
man/averageMassSpectra-functions.Rd
man/plotMsiSlice-methods.Rd
man/filterPeaks-functions.Rd
man/binPeaks-functions.Rd
man/labelPeaks-methods.Rd
man/mergeMassPeaks-functions.Rd
man/intensityMatrix-functions.Rd
man/match.closest.Rd
man/alignSpectra-functions.Rd
man/AbstractMassObject-class.Rd
man/fiedler2009subset.Rd
man/MassPeaks-class.Rd
man/createMassSpectrum-functions.Rd
man/MALDIquant-parallel.Rd
man/isMassObjectList-functions.Rd
man/MALDIquant-package.Rd
man/detectPeaks-methods.Rd
man/monoisotopicPeaks-methods.Rd
man/calibrateIntensity-methods.Rd
man/removeBaseline-methods.Rd
man/transformIntensity-methods.Rd
man/referencePeaks-functions.Rd
man/MassSpectrum-class.Rd
man/smoothIntensity-methods.Rd
man/MALDIquant-deprecated.Rd
MALDIquant documentation built on May 30, 2017, 12:37 a.m.