MALDIquant: MassSpectrum-class – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

MassSpectrum-class

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 mail@sebastiangibb.de

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)

MALDIquant

Quantitative Analysis of Mass Spectrometry Data

v1.19.3

GPL (>= 3)

Authors

Sebastian Gibb [aut, cre] (<https://orcid.org/0000-0001-7406-4443>), Korbinian Strimmer [ths] (<https://orcid.org/0000-0001-7917-2056>)

Initial release

2019-05-12