MALDIquant (version 1.18)

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.

See Also

'>MassPeaks, '>MassSpectrum, plot,AbstractMassObject,missing-method, transformIntensity,AbstractMassObject-method, trim,AbstractMassObject,numeric-method

Website: http://strimmerlab.org/software/maldiquant/

Examples

# NOT RUN {
## 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]
# }