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MALDIquant (version 1.9)

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

1.9

License

GPL (>= 3)

Issues

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Repository

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

Maintainer

Sebastian Gibb

Last Published

January 14th, 2014

Functions in MALDIquant (1.9)

.estimateBaselineConvexHull

Estimates the baseline by a Convex Hull.

Tests for MassSpectrum or MassPeaks object.

.estimateBaselineTopHat

Estimates the baseline by TopHat filter.

calibrateIntensity-methods

Calibrates intensities of a MassSpectrum object.

warpMassSpectra

Run warping functions on AbstractMassObject objects.

.estimateBaselineSnip

Estimates the baseline by SNIP algorithm.

Align MassSpectrum objects.

MALDIquant-package

Quantitative Analysis of Mass Spectrometry Data

transformIntensity-methods

Transforms intensities of an AbstractMassObject object.

findEmptyMassObjects

Finds or removes empty AbstractMassObject objects in a list.

averageMassSpectra

Averages MassSpectrum objects.

estimateNoise-methods

Estimates the noise of a MassSpectrum object.

Merges MassPeaks objects.

detectPeaks-methods

Detects peaks in a MassSpectrum object.

MALDIquant-deprecated

Deprecated Functions/Methods in Package MALDIquant

MassPeaks-class

Class "MassPeaks"

createMassPeaks

Creates a MassPeaks object.

isMassSpectrumList

Tests a list of MassSpectrum or MassPeaks objects.

removeBaseline-methods

Removes the baseline of a MassSpectrum object.

estimateBaseline-methods

Estimates the baseline of a MassSpectrum object.

smoothIntensity-methods

Smoothes intensities of a MassSpectrum object.

.estimateBaselineMedian

Estimates the baseline by moving estimators.

Align Peaks into discrete bins.

Savitzky-Golay Smoothing Filter

MassSpectrum-class

Class "MassSpectrum"

Creates a reference MassPeaks object.

.estimateNoiseMad

Estimates the noise by MAD.

.estimateNoiseSuperSmoother

Estimates the noise by Friedman's Super Smoother.

Trim an AbstractMassObject object.

Removes less frequent peaks.

Moving Average Smoothing Filter

AbstractMassObject-class

Class "AbstractMassObject"

createMassSpectrum

Creates a MassSpectrum object.

labelPeaks-methods

Draws peak labels to plot.

Plots an AbstractMassObject object.

fiedler2009subset

Example Mass Spectra (raw)

determineWarpingFunctions

Determine warping functions of MassPeaks objects.

intensityMatrix

Converts a list of MassPeaks objects into a matrix.