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MALDIquant (version 1.8)

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

1.8

License

GPL (>= 3)

Issues

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Repository

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

Maintainer

Sebastian Gibb

Last Published

September 8th, 2013

Functions in MALDIquant (1.8)

.estimateNoiseMad

Estimates the noise by MAD.

Tests for MassSpectrum or MassPeaks object.

removeBaseline-methods

Removes the baseline of a MassSpectrum object.

Moving Average Smoothing Filter

AbstractMassObject-class

Class "AbstractMassObject"

estimateNoise-methods

Estimates the noise of a MassSpectrum object.

MALDIquant-deprecated

Deprecated Functions/Methods in Package MALDIquant

averageMassSpectra

Averages MassSpectrum objects.

labelPeaks-methods

Draws peak labels to plot.

MassSpectrum-class

Class "MassSpectrum"

Plots an AbstractMassObject object.

estimateBaseline-methods

Estimates the baseline of a MassSpectrum object.

isMassSpectrumList

Tests a list of MassSpectrum or MassPeaks objects.

.estimateBaselineMedian

Estimates the baseline by moving estimators.

createMassPeaks

Creates a MassPeaks object.

Removes less frequently peaks.

warpMassSpectra

Run warping functions on AbstractMassObject objects.

.estimateNoiseSuperSmoother

Estimates the noise by Friedman's Super Smoother.

calibrateIntensity-methods

Calibrates intensities of a MassSpectrum object.

determineWarpingFunctions

Determine warping functions of MassPeaks objects.

MALDIquant-internal

Internal MALDIquant Functions

findEmptyMassObjects

Finds or removes empty AbstractMassObject objects in a list.

MALDIquant-package

Quantitative Analysis of Mass Spectrometry Data

detectPeaks-methods

Detects peaks in a MassSpectrum object.

Trim an AbstractMassObject object.

Align Peaks into discrete bins.

transformIntensity-methods

Transforms intensities of an AbstractMassObject object.

createMassSpectrum

Creates a MassSpectrum object.

Creates a reference MassPeaks object.

Merges MassPeaks objects.

fiedler2009subset

Example Mass Spectra (raw)

.estimateBaselineSnip

Estimates the baseline by SNIP algorithm.

.estimateBaselineConvexHull

Estimates the baseline by a Convex Hull.

smoothIntensity-methods

Smoothes intensities of a MassSpectrum object.

intensityMatrix

Converts a list of AbstractMassObject objects into a matrix.

.estimateBaselineTopHat

Estimates the baseline by TopHat filter.

MassPeaks-class

Class "MassPeaks"

Savitzky-Golay Smoothing Filter