MALDIquant: Quantitative Analysis of Mass Spectrometry Data

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.

AuthorSebastian Gibb [aut, cre], Korbinian Strimmer [ths]
Date of publication2017-01-11 00:43:58
MaintainerSebastian Gibb <mail@sebastiangibb.de>
LicenseGPL (>= 3)
Version1.16.1
http://strimmerlab.org/software/maldiquant/ https://github.com/sgibb/MALDIquant/

View on CRAN

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
[,AbstractMassObject,logical,missing-method Man page
[,AbstractMassObject,numeric,missing-method Man page
alignSpectra Man page
as.matrix,AbstractMassObject-method Man page
averageMassSpectra Man page
binPeaks Man page
calibrateIntensity Man page
calibrateIntensity,list-method Man page
calibrateIntensity,MassSpectrum-method Man page
coordinates Man page
coordinates<- Man page
coordinates<-,AbstractMassObject,matrix-method Man page
coordinates,AbstractMassObject-method Man page
coordinates<-,AbstractMassObject,numeric-method Man page
coordinates<-,list,matrix-method Man page
coordinates,list-method Man page
createMassPeaks Man page
createMassSpectrum Man page
detectPeaks Man page
detectPeaks,list-method Man page
detectPeaks,MassSpectrum-method Man page
determineWarpingFunctions Man page
estimateBaseline Man page
estimateBaseline,MassSpectrum-method Man page
estimateNoise Man page
estimateNoise,MassSpectrum-method Man page
fiedler2009subset Man page
filterPeaks Man page
findEmptyMassObjects Man page
intensity Man page
intensity<- Man page
intensity,AbstractMassObject-method Man page
intensity<-,AbstractMassObject,numeric-method Man page
intensityMatrix Man page
isEmpty Man page
isEmpty,AbstractMassObject-method Man page
isMassPeaks Man page
isMassPeaksList Man page
isMassSpectrum Man page
isMassSpectrumList Man page
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
MALDIquant Man page
MALDIquant-defunct Man page
MALDIquant-deprecated Man page
MALDIquant-package Man page
MALDIquant-parallel Man page
mass Man page
mass<- Man page
mass,AbstractMassObject-method Man page
mass<-,AbstractMassObject,numeric-method Man page
MassPeaks Man page
MassPeaks-class Man page
[,MassPeaks,logical,missing-method Man page
[,MassPeaks,numeric,missing-method Man page
MassSpectrum Man page
MassSpectrum-class Man page
match.closest Man page
mergeMassPeaks Man page
metaData Man page
metaData<- Man page
metaData<-,AbstractMassObject-method Man page
metaData,AbstractMassObject-method Man page
monoisotopicPeaks Man page
monoisotopicPeaks,list-method Man page
monoisotopicPeaks,MassPeaks-method Man page
msiSlices Man page
mz Man page
mz<- Man page
mz,AbstractMassObject-method 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
removeBaseline Man page
removeBaseline,list-method Man page
removeBaseline,MassSpectrum-method Man page
removeEmptyMassObjects Man page
smoothIntensity Man page
smoothIntensity,list-method Man page
smoothIntensity,MassSpectrum-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
warpMassSpectra Man page

Files

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

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