Learn R Programming
⚠️There's a newer version (1.22.3) of this package.Take me there.

MALDIquant (version 1.22)

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.

Copy Link

Version

Install

install.packages('MALDIquant')

Monthly Downloads

3,583

Version

1.22

License

GPL (>= 3)

Issues

2

Pull Requests

3

Stars

66

Forks

25

Maintainer

Sebastian Gibb

Last Published

November 10th, 2022

Functions in MALDIquant (1.22)

MALDIquant-defunct

Removed Functions/Methods in Package MALDIquant
alignSpectra

Align MassSpectrum objects.
determineWarpingFunctions

Determine warping functions of MassPeaks objects.
MassPeaks-class

Class "MassPeaks"
findEmptyMassObjects

Finds or removes empty AbstractMassObject objects in a list.
filterPeaks

Removes less frequent peaks.
binPeaks

Align Peaks into discrete bins.
createMassPeaks

Creates a MassPeaks object.
MALDIquant-parallel

Parallel Support in Package MALDIquant
calibrateIntensity-methods

Calibrates intensities of a MassSpectrum object.
estimateNoise-methods

Estimates the noise 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.
createMassSpectrum

Creates a MassSpectrum object.
match.closest

Relaxed Value Matching
mergeMassPeaks

Merges MassPeaks objects.
monoisotopicPeaks-methods

Finds monoisotopic peaks in a MassPeaks object.
msiSlices

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

Draws peak labels to plot.
isMassSpectrumList

Tests a list of MassSpectrum or MassPeaks objects.
isMassSpectrum

Tests for MassSpectrum or MassPeaks object.
intensityMatrix

Converts a list of MassPeaks objects into a matrix.
transformIntensity-methods

Transforms intensities of an AbstractMassObject object.
smoothIntensity-methods

Smoothes intensities of a MassSpectrum object.
trim-methods

Trim an AbstractMassObject object.
warpMassSpectra

Run warping functions on AbstractMassObject objects.
plot-methods

Plots an AbstractMassObject object.
referencePeaks

Creates a reference MassPeaks object.
plotMsiSlice-methods

Plots a Mass Spectrometry Imaging dataset.
removeBaseline-methods

Removes the baseline of a MassSpectrum object.
MALDIquant-package

Quantitative Analysis of Mass Spectrometry Data
AbstractMassObject-class

Class "AbstractMassObject"
MassSpectrum-class

Class "MassSpectrum"
averageMassSpectra

Averages MassSpectrum objects.
MALDIquant-deprecated

Deprecated Functions/Methods in Package MALDIquant