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MALDIquant (version 1.0)

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

1.0

License

GPL (>= 3)

Maintainer

Sebastian Gibb

Last Published

March 28th, 2012

Functions in MALDIquant (1.0)

AbstractMassObject-class

Class "AbstractMassObject"
MassSpectrum-class

Class "MassSpectrum"
MassPeaks-class

Class "MassPeaks"
calibrate

Calibrates MassObject objects.
isMassObject

Tests for AbstractMassObject objects.
intensityMatrix

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

Removes the baseline of a MassSpectrum object.
findLocalMaxima-methods

Find local maxima in a MassSpectrum object.
.estimateBaselineConvexHull

Estimates the baseline by a Convex Hull.
spectra

Example Mass Spectra (raw)
transformIntensity-methods

Transforms Intensities of an AbstractMassObject object.
labelPeaks-methods

Draws peak labels to plot.
.estimateBaselineMedian

Estimates the baseline by moving estimators.
warpMassSpectra

Run warping functions on AbstractMassObject objects.
imputeMass-methods

Imputes missing mass values to a MassSpectrum object.
MALDIquant-package

Quantitative Analysis of Mass Spectrometric Data
findEmptyMassObjects

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

Estimates the noise of a MassSpectrum object.
estimateBaseline-methods

Estimates the baseline of a MassSpectrum object.
MALDIquant-internal

Internal MALDIquant Functions
detectPeaks-methods

Detects peaks in a MassSpectrum object.
.estimateBaselineSnip

Estimates the baseline by SNIP algorithm.
createMassSpectrum

Creates a MassSpectrum object.
determineWarpingFunctions

Determine warping functions of MassPeaks objects.
binPeaks

Align Peaks into discrete bins.
filterPeaks

Removes less frequently peaks.
peaks

Example Mass Spectra (extracted peaks)
createMassPeaks

Creates a MassPeaks object.
mergeMassSpectra

Merges MassPeaks or MassSpectrum objects.
plot-methods

Plots an AbstractMassObject object.
isMassObjectList

Tests a list of AbstractMassObject objects.
referencePeaks

Creates a reference MassPeaks object.