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MALDIquant (version 1.3)

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

1.3

License

GPL (>= 3)

Maintainer

Sebastian Gibb

Last Published

September 16th, 2012

Functions in MALDIquant (1.3)

createMassPeaks

Creates a MassPeaks object.
detectPeaks-methods

Detects peaks in a MassSpectrum object.
transformIntensity-methods

Transforms intensities of an AbstractMassObject object.
createMassSpectrum

Creates a MassSpectrum object.
filterPeaks

Removes less frequently peaks.
plot-methods

Plots an AbstractMassObject object.
removeBaseline-methods

Removes the baseline of a MassSpectrum object.
MassPeaks-class

Class "MassPeaks"
.estimateBaselineMedian

Estimates the baseline by moving estimators.
mergeMassSpectra

Merges MassPeaks or MassSpectrum objects.
.estimateBaselineSnip

Estimates the baseline by SNIP algorithm.
trim-methods

Trim an AbstractMassObject object.
MassSpectrum-class

Class "MassSpectrum"
labelPeaks-methods

Draws peak labels to plot.
binPeaks

Align Peaks into discrete bins.
determineWarpingFunctions

Determine warping functions of MassPeaks objects.
findEmptyMassObjects

Finds or removes empty AbstractMassObject objects in a list.
calibrate-methods

Calibrates intensity matrix.
fiedler2009subset

Example Mass Spectra (raw)
AbstractMassObject-class

Class "AbstractMassObject"
isMassObject

Tests for AbstractMassObject objects.
intensityMatrix

Converts a list MassObject objects into a matrix.
estimateNoise-methods

Estimates the noise of a MassSpectrum object.
MALDIquant-internal

Internal MALDIquant Functions
estimateBaseline-methods

Estimates the baseline of a MassSpectrum object.
MALDIquant-package

Quantitative Analysis of Mass spectrometry Data
isMassObjectList

Tests a list of AbstractMassObject objects.
.estimateBaselineConvexHull

Estimates the baseline by a Convex Hull.
warpMassSpectra

Run warping functions on AbstractMassObject objects.
imputeMass-methods

Imputes missing mass values to a MassSpectrum object.
standardizeTotalIonCurrent-methods

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

Creates a reference MassPeaks object.