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MALDIquant (version 1.1)

Quantitative Analysis of Mass Spectrometric Data

Description

MALDIquant provides a complete analysis pipeline for MALDI-TOF and other mass spectrometric data. Distinctive features include baseline subtraction using the SNIP algorithm, peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.

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Version

Install

install.packages('MALDIquant')

Monthly Downloads

5,864

Version

1.1

License

GPL (>= 3)

Maintainer

Sebastian Gibb

Last Published

May 6th, 2012

Functions in MALDIquant (1.1)

.estimateBaselineSnip

Estimates the baseline by SNIP algorithm.

Creates a reference MassPeaks object.

averageMassSpectra

Averages MassSpectrum objects.

fiedler2009subset

Example Mass Spectra (raw)

Plots an AbstractMassObject object.

MassPeaks-class

Class "MassPeaks"

.estimateBaselineTopHat

Estimates the baseline by TopHat filter.

Removes less frequent peaks.

removeBaseline-methods

Removes the baseline of a MassSpectrum object.

createMassSpectrum

Creates a MassSpectrum object.

determineWarpingFunctions

Determine warping functions of MassPeaks objects.

labelPeaks-methods

Draws peak labels to plot.

.estimateBaselineConvexHull

Estimates the baseline by a Convex Hull.

detectPeaks-methods

Detects peaks in a MassSpectrum object.

MALDIquant-package

Quantitative Analysis of Mass Spectrometric Data

findEmptyMassObjects

Finds or removes empty AbstractMassObject objects in a list.

.estimateNoiseMad

Estimates the noise by MAD.

.estimateBaselineMedian

Estimates the baseline by moving estimators.

estimateNoise-methods

Estimates the noise of a MassSpectrum object.

smoothIntensity-methods

Smoothes intensities of a MassSpectrum object.

isMassSpectrumList

Tests a list of MassSpectrum or MassPeaks objects.

Align MassSpectrum objects.

createMassPeaks

Creates a MassPeaks object.

Merges MassPeaks objects.

MassSpectrum-class

Class "MassSpectrum"

Align Peaks into discrete bins.

MALDIquant-defunct

Removed Functions/Methods in Package MALDIquant

estimateBaseline-methods

Estimates the baseline of a MassSpectrum object.

plotMsiSlice-methods

Plots a Mass Spectrometry Imaging dataset.

AbstractMassObject-class

Class "AbstractMassObject"

Trim an AbstractMassObject object.

mergeMassSpectra

Merges MassPeaks or MassSpectrum objects.

MALDIquant-deprecated

Deprecated Functions/Methods in Package MALDIquant

MALDIquant-parallel

Parallel Support in Package MALDIquant

intensityMatrix

Converts a list of MassPeaks objects into a matrix.

Tests for MassSpectrum or MassPeaks object.

transformIntensity-methods

Transforms intensities of an AbstractMassObject object.

calibrateIntensity-methods

Calibrates intensities of a MassSpectrum object.

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

isMassObjectList

Tests a list of AbstractMassObject objects.

warpMassSpectra

Run warping functions on AbstractMassObject objects.

Plots an Imaging Mass Spectrometry dataset.

.estimateNoiseSuperSmoother

Estimates the noise by Friedman's Super Smoother.

imputeMass-methods

Imputes missing mass values to a MassSpectrum object.

Savitzky-Golay Smoothing Filter

MALDIquant-internal

Internal MALDIquant Functions

calibrate-methods

Calibrates intensity matrix.

Moving Average Smoothing Filter

Tests for AbstractMassObject objects.

standardizeTotalIonCurrent-methods

Standardizes the Total Ion Current of a list of AbstractMassObject objects.