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MALDIquant (version 1.12)

Quantitative Analysis of Mass Spectrometry Data

Description

A complete analysis pipeline for MALDI-TOF and other mass spectrometry data. Distinctive features include baseline subtraction methods such as TopHat or 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

1.12

License

GPL (>= 3)

Issues

2

Pull Requests

3

Stars

68

Forks

24

Maintainer

Sebastian Gibb

Last Published

June 11th, 2015

Functions in MALDIquant (1.12)

calibrateIntensity-methods

Calibrates intensities of a MassSpectrum object.
findEmptyMassObjects

Finds or removes empty AbstractMassObject objects in a list.
mergeMassPeaks

Merges MassPeaks objects.
trim-methods

Trim an AbstractMassObject object.
MassPeaks-class

Class "MassPeaks"
alignSpectra

Align MassSpectrum objects.
averageMassSpectra

Averages MassSpectrum objects.
estimateNoise-methods

Estimates the noise of a MassSpectrum object.
MALDIquant-package

Quantitative Analysis of Mass Spectrometry Data
isMassSpectrumList

Tests a list of MassSpectrum or MassPeaks objects.
createMassPeaks

Creates a MassPeaks object.
intensityMatrix

Converts a list of MassPeaks objects into a matrix.
MALDIquant-deprecated

Deprecated Functions/Methods in Package MALDIquant
createMassSpectrum

Creates a MassSpectrum object.
transformIntensity-methods

Transforms intensities of an AbstractMassObject object.
isMassSpectrum

Tests for MassSpectrum or MassPeaks object.
filterPeaks

Removes less frequent peaks.
warpMassSpectra

Run warping functions on AbstractMassObject objects.
AbstractMassObject-class

Class "AbstractMassObject"
referencePeaks

Creates a reference MassPeaks object.
determineWarpingFunctions

Determine warping functions of MassPeaks objects.
plotMsiSlice-methods

Plots a Mass Spectrometry Imaging dataset.
smoothIntensity-methods

Smoothes intensities of a MassSpectrum object.
estimateBaseline-methods

Estimates the baseline of a MassSpectrum object.
fiedler2009subset

Example Mass Spectra (raw)
detectPeaks-methods

Detects peaks in a MassSpectrum object.
removeBaseline-methods

Removes the baseline of a MassSpectrum object.
plot-methods

Plots an AbstractMassObject object.
MALDIquant-parallel

Parallel Support in Package MALDIquant
MassSpectrum-class

Class "MassSpectrum"
msiSlices

Turn a list of AbstractMassObjects into a mass spectrometry imaging slice.
labelPeaks-methods

Draws peak labels to plot.
MALDIquant-defunct

Removed Functions/Methods in Package MALDIquant
binPeaks

Align Peaks into discrete bins.