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MALDIquant (version 1.13)

Quantitative Analysis of Mass Spectrometry Data

Description

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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Version

Install

install.packages('MALDIquant')

Monthly Downloads

5,864

Version

1.13

License

GPL (>= 3)

Issues

2

Pull Requests

3

Stars

68

Forks

24

Maintainer

Sebastian Gibb

Last Published

September 16th, 2015

Functions in MALDIquant (1.13)

referencePeaks

Creates a reference MassPeaks object.
msiSlices

Turn a list of AbstractMassObjects into a mass spectrometry imaging slice.
MassSpectrum-class

Class "MassSpectrum"
isMassSpectrum

Tests for MassSpectrum or MassPeaks object.
alignSpectra

Align MassSpectrum objects.
removeBaseline-methods

Removes the baseline of a MassSpectrum object.
MassPeaks-class

Class "MassPeaks"
MALDIquant-defunct

Removed Functions/Methods in Package MALDIquant
createMassPeaks

Creates a MassPeaks object.
calibrateIntensity-methods

Calibrates intensities of a MassSpectrum object.
MALDIquant-parallel

Parallel Support in Package MALDIquant
binPeaks

Align Peaks into discrete bins.
labelPeaks-methods

Draws peak labels to plot.
determineWarpingFunctions

Determine warping functions of MassPeaks objects.
isMassSpectrumList

Tests a list of MassSpectrum or MassPeaks objects.
MALDIquant-deprecated

Deprecated Functions/Methods in Package MALDIquant
AbstractMassObject-class

Class "AbstractMassObject"
mergeMassPeaks

Merges MassPeaks objects.
averageMassSpectra

Averages MassSpectrum objects.
estimateBaseline-methods

Estimates the baseline of a MassSpectrum object.
plot-methods

Plots an AbstractMassObject object.
fiedler2009subset

Example Mass Spectra (raw)
trim-methods

Trim an AbstractMassObject object.
estimateNoise-methods

Estimates the noise of a MassSpectrum object.
MALDIquant-package

Quantitative Analysis of Mass Spectrometry Data
createMassSpectrum

Creates a MassSpectrum object.
findEmptyMassObjects

Finds or removes empty AbstractMassObject objects in a list.
smoothIntensity-methods

Smoothes intensities of a MassSpectrum object.
filterPeaks

Removes less frequent peaks.
warpMassSpectra

Run warping functions on AbstractMassObject objects.
transformIntensity-methods

Transforms intensities of an AbstractMassObject object.
detectPeaks-methods

Detects peaks in a MassSpectrum object.
plotMsiSlice-methods

Plots a Mass Spectrometry Imaging dataset.
intensityMatrix

Converts a list of MassPeaks objects into a matrix.