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.

Author
Sebastian Gibb [aut, cre], Korbinian Strimmer [ths]
Date of publication
2016-06-25 19:46:10
Maintainer
Sebastian Gibb <mail@sebastiangibb.de>
License
GPL (>= 3)
Version
1.15
URLs

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"
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.

Files in this package

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_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_which.closest-functions.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/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/which.closest-functions.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/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