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MALDIquant (version 1.7)

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 methods such as TopHat or SNIP, peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.

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Install

install.packages('MALDIquant')

Monthly Downloads

5,864

Version

1.7

License

GPL (>= 3)

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Repository

http://strimmerlab.org/software/maldiquant/ https://github.com/sgibb/MALDIquant/

Maintainer

Sebastian Gibb

Last Published

May 23rd, 2013

Functions in MALDIquant (1.7)

Interactive plot of MassSpectrum objects.

AbstractMassObject-class

Class "AbstractMassObject"

MALDIquant-internal

Internal MALDIquant Functions

.estimateNoiseMad

Estimates the noise by MAD.

.estimateNoiseSuperSmoother

Estimates the noise by Friedman's Super Smoother.

transformIntensity-methods

Transforms intensities of an AbstractMassObject object.

labelPeaks-methods

Draws peak labels to plot.

fiedler2009subset

Example Mass Spectra (raw)

createMassSpectrum

Creates a MassSpectrum object.

Moving Average Smoothing Filter

Tests for AbstractMassObject objects.

MassPeaks-class

Class "MassPeaks"

detectPeaks-methods

Detects peaks in a MassSpectrum object.

findEmptyMassObjects

Finds or removes empty AbstractMassObject objects in a list.

.estimateBaselineConvexHull

Estimates the baseline by a Convex Hull.

Savitzky-Golay Smoothing Filter

Plots an AbstractMassObject object.

removeBaseline-methods

Removes the baseline of a MassSpectrum object.

mergeMassSpectra

Merges MassPeaks or MassSpectrum objects.

isMassObjectList

Tests a list of AbstractMassObject objects.

.estimateBaselineMedian

Estimates the baseline by moving estimators.

imputeMass-methods

Imputes missing mass values to a MassSpectrum object.

standardizeTotalIonCurrent-methods

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

Align Peaks into discrete bins.

MALDIquant-package

Quantitative Analysis of Mass Spectrometry Data

estimateBaseline-methods

Estimates the baseline of a MassSpectrum object.

Removes less frequently peaks.

createMassPeaks

Creates a MassPeaks object.

intensityMatrix

Converts a list of AbstractMassObject objects into a matrix.

estimateNoise-methods

Estimates the noise of a MassSpectrum object.

.estimateBaselineSnip

Estimates the baseline by SNIP algorithm.

MassSpectrum-class

Class "MassSpectrum"

Trim an AbstractMassObject object.

determineWarpingFunctions

Determine warping functions of MassPeaks objects.

calibrate-methods

Calibrates intensity matrix.

.estimateBaselineTopHat

Estimates the baseline by TopHat filter.

Creates a reference MassPeaks object.

warpMassSpectra

Run warping functions on AbstractMassObject objects.