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MALDIquant (version 1.11)

Quantitative Analysis of Mass Spectrometry Data

Description

MALDIquant provides 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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Install

install.packages('MALDIquant')

Monthly Downloads

5,864

Version

1.11

License

GPL (>= 3)

Issues

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Repository

http://strimmerlab.org/software/maldiquant/ https://github.com/sgibb/MALDIquant/

Maintainer

Sebastian Gibb

Last Published

August 11th, 2014

Functions in MALDIquant (1.11)

createMassPeaks

Creates a MassPeaks object.

intensityMatrix

Converts a list of MassPeaks objects into a matrix.

Align Peaks into discrete bins.

calibrateIntensity-methods

Calibrates intensities of a MassSpectrum object.

removeBaseline-methods

Removes the baseline of a MassSpectrum object.

isMassSpectrumList

Tests a list of MassSpectrum or MassPeaks objects.

labelPeaks-methods

Draws peak labels to plot.

Plots an Imaging Mass Spectrometry dataset.

smoothIntensity-methods

Smoothes intensities of a MassSpectrum object.

AbstractMassObject-class

Class "AbstractMassObject"

estimateNoise-methods

Estimates the noise of a MassSpectrum object.

transformIntensity-methods

Transforms intensities of an AbstractMassObject object.

Tests for MassSpectrum or MassPeaks object.

Creates a reference MassPeaks object.

MALDIquant-package

Quantitative Analysis of Mass Spectrometry Data

MassPeaks-class

Class "MassPeaks"

Trim an AbstractMassObject object.

createMassSpectrum

Creates a MassSpectrum object.

averageMassSpectra

Averages MassSpectrum objects.

MALDIquant-defunct

Removed Functions/Methods in Package MALDIquant

MassSpectrum-class

Class "MassSpectrum"

detectPeaks-methods

Detects peaks in a MassSpectrum object.

Align MassSpectrum objects.

fiedler2009subset

Example Mass Spectra (raw)

estimateBaseline-methods

Estimates the baseline of a MassSpectrum object.

Removes less frequent peaks.

warpMassSpectra

Run warping functions on AbstractMassObject objects.

MALDIquant-deprecated

Deprecated Functions/Methods in Package MALDIquant

Plots an AbstractMassObject object.

determineWarpingFunctions

Determine warping functions of MassPeaks objects.

findEmptyMassObjects

Finds or removes empty AbstractMassObject objects in a list.

Merges MassPeaks objects.