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MALDIquant (version 1.6)

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

5,489

Version

1.6

License

GPL (>= 3)

Issues

2

Pull Requests

3

Stars

68

Forks

24

Maintainer

Sebastian Gibb

Last Published

March 1st, 2013

Functions in MALDIquant (1.6)

AbstractMassObject-class

Class "AbstractMassObject"
.estimateBaselineConvexHull

Estimates the baseline by a Convex Hull.
MALDIquant-package

Quantitative Analysis of Mass Spectrometry Data
filterPeaks

Removes less frequently peaks.
.estimateNoiseMad

Estimates the noise by MAD.
trim-methods

Trim an AbstractMassObject object.
findEmptyMassObjects

Finds or removes empty AbstractMassObject objects in a list.
referencePeaks

Creates a reference MassPeaks object.
estimateBaseline-methods

Estimates the baseline of a MassSpectrum object.
createMassSpectrum

Creates a MassSpectrum object.
estimateNoise-methods

Estimates the noise of a MassSpectrum object.
determineWarpingFunctions

Determine warping functions of MassPeaks objects.
fiedler2009subset

Example Mass Spectra (raw)
movingAverage

Moving Average
createMassPeaks

Creates a MassPeaks object.
calibrate-methods

Calibrates intensity matrix.
transformIntensity-methods

Transforms intensities of an AbstractMassObject object.
binPeaks

Align Peaks into discrete bins.
.estimateBaselineMedian

Estimates the baseline by moving estimators.
.estimateBaselineSnip

Estimates the baseline by SNIP algorithm.
isMassObject

Tests for AbstractMassObject objects.
.estimateBaselineTopHat

Estimates the baseline by TopHat filter.
labelPeaks-methods

Draws peak labels to plot.
warpMassSpectra

Run warping functions on AbstractMassObject objects.
iplot-methods

Interactive plot of MassSpectrum objects.
plot-methods

Plots an AbstractMassObject object.
standardizeTotalIonCurrent-methods

Standardizes the Total Ion Current of a list of AbstractMassObject objects.
removeBaseline-methods

Removes the baseline of a MassSpectrum object.
isMassObjectList

Tests a list of AbstractMassObject objects.
mergeMassSpectra

Merges MassPeaks or MassSpectrum objects.
detectPeaks-methods

Detects peaks in a MassSpectrum object.
MALDIquant-internal

Internal MALDIquant Functions
.estimateNoiseSuperSmoother

Estimates the noise by Friedman's Super Smoother.
MassPeaks-class

Class "MassPeaks"
imputeMass-methods

Imputes missing mass values to a MassSpectrum object.
intensityMatrix

Converts a list of AbstractMassObject objects into a matrix.
MassSpectrum-class

Class "MassSpectrum"