MALDIquant: AbstractMassObject-class – R documentation

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

AbstractMassObject-class

Class "AbstractMassObject"

Description

AbstractMassObject is an abstract (means pure virtual) class. It is the parent class of MassSpectrum and MassPeaks. It shouldn't create or handle by the user because it is for internal use only.

Derived classes

MassPeaks, MassSpectrum

Slots

mass:: numeric, mass or mass-to-charge ratio
intensity:: numeric, intensities for measured mass-to-charge ratios
metaData:: list, some metadata to describe the spectrum

Methods

[: signature(x = "AbstractMassObject", i = "numeric"): Extracts a range of an AbstractMassObject object and returns a new one.
as.matrix: signature(x = "AbstractMassObject"): Converts an AbstractMassObject object to a matrix with 2 columns (mass, intensity).
coordinates: signature(object = "AbstractMassObject"): Accessor function for coordinates stored in object generated from imaging mass spectrometry data.
coordinates<-: signature(object = "AbstractMassObject", value = "numeric|matrix") Replacement function for coordinates used in imaging mass spectrometry datasets.
intensity: signature(object = "AbstractMassObject"): Accessor function for slot intensity.
intensity<-: signature(object = "AbstractMassObject", value = "numeric") Replacement function for slot intensity.
isEmpty: signature(object = "AbstractMassObject"): Returns TRUE if length of intensity is 0 or all intensity values are 0.
length: signature(x = "AbstractMassObject"): Returns length of slot intensity.
lines: signature(x = "AbstractMassObject"): Extented function for adding AbstractMassObject object as a line to a specific plot. See lines for details.
mass: signature(object = "AbstractMassObject"): Accessor function for slot mass.
mass<-: signature(object = "AbstractMassObject", value = "numeric") Replacement function for slot mass.
mz: signature(object = "AbstractMassObject"): Accessor function for slot mass.
mz<-: signature(object = "AbstractMassObject", value = "numeric") Replacement function for slot mass.
metaData: signature(object = "AbstractMassObject"): Accessor function for slot metaData.
metaData<-: signature(object = "AbstractMassObject"): Replacement function for slot metaData.
plot: signature(x = "AbstractMassObject", y = "missing"): Extented function for plotting an AbstractMassObject object. See plot,AbstractMassObject,missing-method for details.
points: signature(x = "AbstractMassObject"): Extented function for adding AbstractMassObject object as points to a specific plot. See points for details.
trim: signature(object = "AbstractMassObject", range = "numeric"): Trim an AbstractMassObject object. See trim,AbstractMassObject,numeric-method for details.
transformIntensity: signature(object = "AbstractMassObject"): Transforms the intensities of an AbstractMassObject object. See transformIntensity,AbstractMassObject-method for details.

Author(s)

Sebastian Gibb mail@sebastiangibb.de

Examples

## load package
library("MALDIquant")

## create example spectrum
s <- createMassSpectrum(mass=1:10, intensity=11:20,
                        metaData=list(name="Example Spectrum"))

## get intensity
intensity(s)

## get mass
mass(s)

## get metaData
metaData(s)

## replace metaData
metaData(s) <- list(name="Spectrum")

## trim spectrum
trim(s, c(2, 9))

## select a range
s[3:6]

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