AbstractMassObject-class | R Documentation |
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.
MassPeaks
,
MassSpectrum
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
signature(x = "AbstractMassObject", i = "numeric")
:
Extracts a range of an AbstractMassObject
object
and returns a new one.
signature(x = "AbstractMassObject")
:
Converts an AbstractMassObject
object to a
matrix with 2 columns (mass
, intensity
).
signature(object = "AbstractMassObject")
:
Accessor function for coordinates stored in object generated from imaging
mass spectrometry data.
signature(object = "AbstractMassObject",
value = "numeric|matrix")
Replacement function for coordinates used in imaging mass spectrometry
datasets.
signature(object = "AbstractMassObject")
:
Accessor function for slot intensity
.
signature(object = "AbstractMassObject",
value = "numeric")
Replacement function for slot intensity
.
signature(object = "AbstractMassObject")
:
Returns TRUE
if length of intensity
is 0 or all
intensity
values are 0.
signature(x = "AbstractMassObject")
:
Returns length of slot intensity
.
signature(x = "AbstractMassObject")
:
Extented function for adding AbstractMassObject
object as a
line to a specific plot.
See lines
for details.
signature(object = "AbstractMassObject")
:
Accessor function for slot mass
.
signature(object = "AbstractMassObject",
value = "numeric")
Replacement function for slot mass
.
signature(object = "AbstractMassObject")
:
Accessor function for slot mass
.
signature(object = "AbstractMassObject",
value = "numeric")
Replacement function for slot mass
.
signature(object = "AbstractMassObject")
:
Accessor function for slot metaData
.
signature(object = "AbstractMassObject")
:
Replacement function for slot metaData
.
signature(x = "AbstractMassObject", y = "missing")
:
Extented function for plotting an AbstractMassObject
object.
See plot,AbstractMassObject,missing-method
for
details.
signature(x = "AbstractMassObject")
:
Extented function for adding
AbstractMassObject
object as points
to a specific plot.
See points
for details.
signature(object = "AbstractMassObject",
range = "numeric")
: Trim an AbstractMassObject
object. See trim,AbstractMassObject,numeric-method
for details.
signature(object = "AbstractMassObject")
:
Transforms the intensities of an AbstractMassObject
object.
See transformIntensity,AbstractMassObject-method
for details.
Sebastian Gibb mail@sebastiangibb.de
MassPeaks
,
MassSpectrum
,
plot,AbstractMassObject,missing-method
,
transformIntensity,AbstractMassObject-method
,
trim,AbstractMassObject,numeric-method
Website: https://strimmerlab.github.io/software/maldiquant/
## 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]
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