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MALDIquant (version 1.4)

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

1.4

License

GPL (>= 3)

Issues

2

Pull Requests

3

Stars

68

Forks

24

Maintainer

Sebastian Gibb

Last Published

October 30th, 2012

Functions in MALDIquant (1.4)

MassSpectrum-class

Class "MassSpectrum"
calibrate-methods

Calibrates intensity matrix.
createMassPeaks

Creates a MassPeaks object.
.estimateBaselineConvexHull

Estimates the baseline by a Convex Hull.
MassPeaks-class

Class "MassPeaks"
imputeMass-methods

Imputes missing mass values to a MassSpectrum object.
.estimateBaselineSnip

Estimates the baseline by SNIP algorithm.
labelPeaks-methods

Draws peak labels to plot.
mergeMassSpectra

Merges MassPeaks or MassSpectrum objects.
determineWarpingFunctions

Determine warping functions of MassPeaks objects.
estimateBaseline-methods

Estimates the baseline of a MassSpectrum object.
transformIntensity-methods

Transforms intensities of an AbstractMassObject object.
MALDIquant-internal

Internal MALDIquant Functions
plot-methods

Plots an AbstractMassObject object.
createMassSpectrum

Creates a MassSpectrum object.
detectPeaks-methods

Detects peaks in a MassSpectrum object.
MALDIquant-package

Quantitative Analysis of Mass spectrometry Data
AbstractMassObject-class

Class "AbstractMassObject"
filterPeaks

Removes less frequently peaks.
.estimateBaselineMedian

Estimates the baseline by moving estimators.
estimateNoise-methods

Estimates the noise of a MassSpectrum object.
removeBaseline-methods

Removes the baseline of a MassSpectrum object.
.estimateNoiseSuperSmoother

Estimates the noise by Friedman's Super Smoother.
warpMassSpectra

Run warping functions on AbstractMassObject objects.
referencePeaks

Creates a reference MassPeaks object.
intensityMatrix

Converts a list MassObject objects into a matrix.
isMassObjectList

Tests a list of AbstractMassObject objects.
findEmptyMassObjects

Finds or removes empty AbstractMassObject objects in a list.
.estimateNoiseMad

Estimates the noise by MAD.
binPeaks

Align Peaks into discrete bins.
trim-methods

Trim an AbstractMassObject object.
isMassObject

Tests for AbstractMassObject objects.
fiedler2009subset

Example Mass Spectra (raw)
standardizeTotalIonCurrent-methods

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