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MALDIquant (version 1.5)

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 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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Install

install.packages('MALDIquant')

Monthly Downloads

5,864

Version

1.5

License

GPL (>= 3)

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Repository

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

Maintainer

Sebastian Gibb

Last Published

December 7th, 2012

Functions in MALDIquant (1.5)

mergeMassSpectra

Merges MassPeaks or MassSpectrum objects.

MALDIquant-internal

Internal MALDIquant Functions

MassPeaks-class

Class "MassPeaks"

warpMassSpectra

Run warping functions on AbstractMassObject objects.

detectPeaks-methods

Detects peaks in a MassSpectrum object.

createMassSpectrum

Creates a MassSpectrum object.

.estimateNoiseMad

Estimates the noise by MAD.

isMassObjectList

Tests a list of AbstractMassObject objects.

labelPeaks-methods

Draws peak labels to plot.

Removes less frequently peaks.

intensityMatrix

Converts a list MassObject objects into a matrix.

Align Peaks into discrete bins.

.estimateBaselineSnip

Estimates the baseline by SNIP algorithm.

Tests for AbstractMassObject objects.

removeBaseline-methods

Removes the baseline of a MassSpectrum object.

estimateNoise-methods

Estimates the noise of a MassSpectrum object.

imputeMass-methods

Imputes missing mass values to a MassSpectrum object.

transformIntensity-methods

Transforms intensities of an AbstractMassObject object.

.estimateNoiseSuperSmoother

Estimates the noise by Friedman's Super Smoother.

fiedler2009subset

Example Mass Spectra (raw)

determineWarpingFunctions

Determine warping functions of MassPeaks objects.

MALDIquant-package

Quantitative Analysis of Mass spectrometry Data

createMassPeaks

Creates a MassPeaks object.

Trim an AbstractMassObject object.

estimateBaseline-methods

Estimates the baseline of a MassSpectrum object.

calibrate-methods

Calibrates intensity matrix.

.estimateBaselineConvexHull

Estimates the baseline by a Convex Hull.

AbstractMassObject-class

Class "AbstractMassObject"

.estimateBaselineMedian

Estimates the baseline by moving estimators.

findEmptyMassObjects

Finds or removes empty AbstractMassObject objects in a list.

Plots an AbstractMassObject object.

MassSpectrum-class

Class "MassSpectrum"

Creates a reference MassPeaks object.

standardizeTotalIonCurrent-methods

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