MassSpectrum-class {MALDIquant}

Class "MassSpectrum"

Description

MassSpectrum represents a single spectrum of a MALDI-TOF mass spectrometry measurement. It provides an easy framework for doing some preprocessing steps like peak detection, baseline correction and much more.

Objects from the Class

createMassSpectrum: Creates a MassSpectrum object.

Extends

Class AbstractMassObject, directly.

Methods

calibrateIntensity

signature(x = "MassSpectrum"): Calibrates the intensity of a MassSpectrum object. See calibrateIntensity,MassSpectrum-method for details.

detectPeaks

signature(x = "MassSpectrum"): Look for local maxima and estimate noise to extract peaks out of a MassSpectrum object. See detectPeaks,MassSpectrum-method for details.

estimateBaseline

signature(x = "MassSpectrum"): Estimates the baseline of a MassSpectrum object. See estimateBaseline,MassSpectrum-method for details.

estimateNoise

signature(x = "MassSpectrum"): Estimates the noise of a MassSpectrum object. See estimateNoise,MassSpectrum-method for details.

isRegular

signature(object = "MassSpectrum"): Returns FALSE if the frequency of mass values with irregular intervals is greater than threshold (because object was measured in centroid mode or some intensity values were filtered).

removeBaseline

signature(x = "MassSpectrum"): Estimates and removes the baseline of a MassSpectrum object. See removeBaseline,MassSpectrum-method for details.

smoothIntensity

signature(object = "MassSpectrum"): Smoothes the intensities of an MassSpectrum object. See smoothIntensity,MassSpectrum-method for details.

totalIonCurrent

signature(object = "MassSpectrum"): Accessor function for Total Ion Current (TIC, area under the curve).

Author(s)

Sebastian Gibb [e-mail]

See Also

createMassSpectrum, calibrateIntensity,MassSpectrum-method, detectPeaks,MassSpectrum-method, estimateBaseline,MassSpectrum-method, estimateNoise,MassSpectrum-method, removeBaseline,MassSpectrum-method, smoothIntensity,MassSpectrum-method, AbstractMassObject

Website: https://strimmerlab.github.io/software/maldiquant/

Examples

## load package
library("MALDIquant")

## create a MassSpectrum object by default constructor
s <- createMassSpectrum(mass=1:100, intensity=rnorm(100)^2,
                        metaData=list(name="example"))

## show some details
s

## plot spectrum
plot(s)

## get TIC
totalIonCurrent(s)

## modify intensity and metaData
intensity(s)[1:50] <- 0
metaData(s) <- list(name="modified example")

## plot again
plot(s)