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MALDIquant (version 1.10)

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

1.10

License

GPL (>= 3)

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Repository

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

Maintainer

Sebastian Gibb

Last Published

April 11th, 2014

Functions in MALDIquant (1.10)

createMassPeaks

Creates a MassPeaks object.

determineWarpingFunctions

Determine warping functions of MassPeaks objects.

Tests for MassSpectrum or MassPeaks object.

estimateBaseline-methods

Estimates the baseline of a MassSpectrum object.

Creates a reference MassPeaks object.

AbstractMassObject-class

Class "AbstractMassObject"

.estimateNoiseMad

Estimates the noise by MAD.

MALDIquant-deprecated

Deprecated Functions/Methods in Package MALDIquant

.estimateBaselineConvexHull

Estimates the baseline by a Convex Hull.

createMassSpectrum

Creates a MassSpectrum object.

MassSpectrum-class

Class "MassSpectrum"

averageMassSpectra

Averages MassSpectrum objects.

warpMassSpectra

Run warping functions on AbstractMassObject objects.

.estimateBaselineSnip

Estimates the baseline by SNIP algorithm.

removeBaseline-methods

Removes the baseline of a MassSpectrum object.

MALDIquant-package

Quantitative Analysis of Mass Spectrometry Data

intensityMatrix

Converts a list of MassPeaks objects into a matrix.

Moving Average Smoothing Filter

MassPeaks-class

Class "MassPeaks"

Merges MassPeaks objects.

Trim an AbstractMassObject object.

findEmptyMassObjects

Finds or removes empty AbstractMassObject objects in a list.

smoothIntensity-methods

Smoothes intensities of a MassSpectrum object.

MALDIquant-defunct

Removed Functions/Methods in Package MALDIquant

detectPeaks-methods

Detects peaks in a MassSpectrum object.

Plots an AbstractMassObject object.

.estimateNoiseSuperSmoother

Estimates the noise by Friedman's Super Smoother.

Align MassSpectrum objects.

Align Peaks into discrete bins.

isMassSpectrumList

Tests a list of MassSpectrum or MassPeaks objects.

labelPeaks-methods

Draws peak labels to plot.

transformIntensity-methods

Transforms intensities of an AbstractMassObject object.

Removes less frequent peaks.

.estimateBaselineMedian

Estimates the baseline by moving estimators.

fiedler2009subset

Example Mass Spectra (raw)

calibrateIntensity-methods

Calibrates intensities of a MassSpectrum object.

.estimateBaselineTopHat

Estimates the baseline by TopHat filter.

Savitzky-Golay Smoothing Filter

estimateNoise-methods

Estimates the noise of a MassSpectrum object.