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.

Install the latest version of this package by entering the following in R:
install.packages("MALDIquant")
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
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

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

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