Spectrum-class.RdVirtual container for spectrum data common to all different types of
spectra. A Spectrum object can not be directly instanciated. Use
"Spectrum1" and "Spectrum2"
instead.
In version 1.19.12, the polarity slot has been added to this
class (previously in "Spectrum1").
msLevel:Object of class "integer" indicating
the MS level: 1 for MS1 level Spectrum1 objects and 2 for MSMSM
Spectrum2 objects. Levels > 2 have not been tested and will be
handled as MS2 spectra.
polarity:Object of class "integer" indicating
the polarity if the ion.
peaksCount:Object of class "integer"
indicating the number of MZ peaks.
rt:Object of class "numeric" indicating the
retention time (in seconds) for the current ions.
tic:Object of class "numeric" indicating the
total ion current, as reported in the original raw data file.
acquisitionNum:Object of class "integer"
corresponding to the acquisition number of the current spectrum.
scanIndex:Object of class "integer" indicating
the scan index of the current spectrum.
mz:Object of class "numeric" of length equal
to the peaks count (see peaksCount slot) indicating the MZ
values that have been measured for the current ion.
intensity:Object of class "numeric" of same
length as mz indicating the intensity at which each mz
datum has been measured.
centroided:Object of class "logical"
indicating if instance is centroided ('TRUE') of uncentroided
('FALSE'). Default is NA.
smoothed:Object of class "logical"
indicating if instance is smoothed ('TRUE') of unsmoothed
('FALSE'). Default is NA.
fromFile:Object of class "integer" referencing
the file the spectrum originates. The file names are stored in the
processingData slot of the "MSnExp" or
"MSnSet" instance that contains the current
"Spectrum" instance.
.__classVersion__:Object of class "Versions"
indicating the version of the Spectrum class. Intended for
developer use and debugging.
Class "Versioned", directly.
acquisitionNum(object)Returns the acquisition number of the spectrum as an integer.
scanIndex(object)Returns the scan index of the spectrum as an integer.
centroided(object)Indicates whether spectrum is
centroided (TRUE), in profile mode (FALSE), or
unkown (NA).
isCentroided(object, k=0.025, qtl=0.9)A heuristic
assessing if a spectrum is in profile or centroided mode. The
function takes the qtlth quantile top peaks, then
calculates the difference between adjacent M/Z value and returns
TRUE if the first quartile is greater than k. (See
MSnbase:::.isCentroided for the code.) The function has
been tuned to work for MS1 and MS2 spectra and data centroided
using different peak picking algorithms, but false positives can
occur. See https://github.com/lgatto/MSnbase/issues/131 for
details. It should however be safe to use is at the experiment
level, assuming that all MS level have the same mode. See
class?MSnExp for an example.
smoothed(object)Indicates whether spectrum is
smoothed (TRUE) or not (FALSE).
centroided(object) <- valueSets the centroided
status of the spectrum object.
smoothed(object) <- valueSets the smoothed
status of the spectrum object.
fromFile(object)Returns the index of the raw data file from which the current instances originates as an integer.
intensity(object)Returns an object of class
numeric containing the intensities of the spectrum.
msLevel(object)Returns an MS level of the spectrum as an integer.
mz(object, ...)Returns an object of class
numeric containing the MZ value of the spectrum
peaks. Additional arguments are currently ignored.
peaksCount(object)Returns the number of peaks (possibly of 0 intensity) as an integer.
rtime(object, ...)Returns the retention time for the spectrum as an integer. Additional arguments are currently ignored.
ionCount(object)Returns the total ion count for the spectrum as a numeric.
tic(object, ...)Returns the total ion current for
the spectrum as a numeric. Additional arguments are currently
ignored. This is the total ion current as originally reported in
the raw data file. To get the current total ion count, use
ionCount.
signature(object = "Spectrum"): Bins Spectrum.
See bin documentation for more details and examples.
signature(object = "Spectrum"): Removes unused 0
intensity data points. See clean documentation
for more details and examples.
signature(x = "Spectrum",
y = "Spectrum"): Compares spectra. See
compareSpectra documentation for more details and
examples.
signature(object = "Spectrum"): Estimates the
noise in a profile spectrum.
See estimateNoise documentation for more
details and examples.
signature(object = "Spectrum"): Performs the peak
picking to generate a centroided spectrum.
See pickPeaks documentation for more
details and examples.
signature(x = "Spectrum", y = "missing"): Plots
intensity against mz.
See plot.Spectrum documentation for more details.
signature(x = "Spectrum", y = "Spectrum"): Plots
two spectra above/below each other.
See plot.Spectrum.Spectrum documentation for more
details.
signature(x = "Spectrum", y = "character"): Plots
an MS2 level spectrum and its highlight the fragmention peaks.
See plot.Spectrum.character documentation for more
details.
signature(object = "Spectrum"): Quatifies
defined peaks in the spectrum.
See quantify documentation for more details.
signature(object = "Spectrum"): Remove
peaks lower that a threshold t. See
removePeaks documentation for more details and
examples.
signature(x = "Spectrum"): Smooths spectrum.
See smooth documentation for more details and examples.
signature(object = "Spectrum"): Displays object
content as text.
signature(object = "Spectrum"): Trims the MZ
range of all the spectra of the MSnExp instance. See
trimMz documentation for more details and
examples.
signature(x = "Spectrum"): Checks if the
x is an empty Spectrum.
signature(object = "Spectrum", "data.frame"):
Coerces the Spectrum object to a two-column
data.frame containing intensities and MZ values.
This is a virtual class and can not be instanciated directly.