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MALDIquant (version 1.2)

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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Version

Install

install.packages('MALDIquant')

Monthly Downloads

5,864

Version

1.2

License

GPL (>= 3)

Maintainer

Sebastian Gibb

Last Published

July 18th, 2012

Functions in MALDIquant (1.2)

MassPeaks-class

Class "MassPeaks"
calibrate-methods

Calibrates intensity matrix.
MALDIquant-internal

Internal MALDIquant Functions
detectPeaks-methods

Detects peaks in a MassSpectrum object.
createMassSpectrum

Creates a MassSpectrum object.
MassSpectrum-class

Class "MassSpectrum"
AbstractMassObject-class

Class "AbstractMassObject"
determineWarpingFunctions

Determine warping functions of MassPeaks objects.
findEmptyMassObjects

Finds or removes empty AbstractMassObject objects in a list.
createMassPeaks

Creates a MassPeaks object.
estimateBaseline-methods

Estimates the baseline of a MassSpectrum object.
binPeaks

Align Peaks into discrete bins.
plot-methods

Plots an AbstractMassObject object.
.estimateBaselineMedian

Estimates the baseline by moving estimators.
MALDIquant-package

Quantitative Analysis of Mass spectrometry Data
referencePeaks

Creates a reference MassPeaks object.
isMassObjectList

Tests a list of AbstractMassObject objects.
imputeMass-methods

Imputes missing mass values to a MassSpectrum object.
fiedler2009subset

Example Mass Spectra (raw)
mergeMassSpectra

Merges MassPeaks or MassSpectrum objects.
transformIntensity-methods

Transforms Intensities of an AbstractMassObject object.
removeBaseline-methods

Removes the baseline of a MassSpectrum object.
estimateNoise-methods

Estimates the noise of a MassSpectrum object.
intensityMatrix

Converts a list MassObject objects into a matrix.
filterPeaks

Removes less frequently peaks.
isMassObject

Tests for AbstractMassObject objects.
labelPeaks-methods

Draws peak labels to plot.
standardizeTotalIonCurrent-methods

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

Run warping functions on AbstractMassObject objects.
.estimateBaselineConvexHull

Estimates the baseline by a Convex Hull.
.estimateBaselineSnip

Estimates the baseline by SNIP algorithm.