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MALDIquant (version 1.22.2)

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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Install

install.packages('MALDIquant')

Monthly Downloads

5,864

Version

1.22.2

License

GPL (>= 3)

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Repository

https://github.com/sgibb/MALDIquant/

Homepage

https://strimmerlab.github.io/software/maldiquant/

Maintainer

Sebastian Gibb

Last Published

January 22nd, 2024

Functions in MALDIquant (1.22.2)

createMassSpectrum

Creates a MassSpectrum object.

determineWarpingFunctions

Determine warping functions of MassPeaks objects.

fiedler2009subset

Example Mass Spectra (raw)

findEmptyMassObjects

Finds or removes empty AbstractMassObject objects in a list.

detectPeaks-methods

Detects peaks in a MassSpectrum object.

estimateNoise-methods

Estimates the noise of a MassSpectrum object.

createMassPeaks

Creates a MassPeaks object.

calibrateIntensity-methods

Calibrates intensities of a MassSpectrum object.

Removes less frequent peaks.

estimateBaseline-methods

Estimates the baseline of a MassSpectrum object.

plotMsiSlice-methods

Plots a Mass Spectrometry Imaging dataset.

Turn a list of AbstractMassObjects into a mass spectrometry imaging slice.

Relaxed Value Matching

monoisotopicPeaks-methods

Finds monoisotopic peaks in a MassPeaks object.

intensityMatrix

Converts a list of MassPeaks objects into a matrix.

Tests for MassSpectrum or MassPeaks object.

isMassSpectrumList

Tests a list of MassSpectrum or MassPeaks objects.

labelPeaks-methods

Draws peak labels to plot.

Plots an AbstractMassObject object.

Creates a reference MassPeaks object.

transformIntensity-methods

Transforms intensities of an AbstractMassObject object.

warpMassSpectra

Run warping functions on AbstractMassObject objects.

smoothIntensity-methods

Smoothes intensities of a MassSpectrum object.

removeBaseline-methods

Removes the baseline of a MassSpectrum object.

Trim an AbstractMassObject object.

Merges MassPeaks objects.

AbstractMassObject-class

Class "AbstractMassObject"

MassPeaks-class

Class "MassPeaks"

Align Peaks into discrete bins.

Align MassSpectrum objects.

MALDIquant-parallel

Parallel Support in Package MALDIquant

averageMassSpectra

Averages MassSpectrum objects.

MassSpectrum-class

Class "MassSpectrum"

MALDIquant-defunct

Removed Functions/Methods in Package MALDIquant

MALDIquant-package

Quantitative Analysis of Mass Spectrometry Data

MALDIquant-deprecated

Deprecated Functions/Methods in Package MALDIquant