Spectrum-class: The "Spectrum" Class

In lgatto/MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

The "Spectrum" Class

Description

Virtual 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").

Slots

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.

Extends

Class "Versioned", directly.

Methods

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) <- value

Sets the centroided status of the spectrum object.

smoothed(object) <- value

Sets 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.

bin

signature(object = "Spectrum"): Bins Spectrum. See bin documentation for more details and examples.

clean

signature(object = "Spectrum"): Removes unused 0 intensity data points. See clean documentation for more details and examples.

compareSpectra

signature(x = "Spectrum", y = "Spectrum"): Compares spectra. See compareSpectra documentation for more details and examples.

estimateNoise

signature(object = "Spectrum"): Estimates the noise in a profile spectrum. See estimateNoise documentation for more details and examples.

pickPeaks

signature(object = "Spectrum"): Performs the peak picking to generate a centroided spectrum. See pickPeaks documentation for more details and examples.

plot

signature(x = "Spectrum", y = "missing"): Plots intensity against mz. See plot.Spectrum documentation for more details.

plot

signature(x = "Spectrum", y = "Spectrum"): Plots two spectra above/below each other. See plot.Spectrum.Spectrum documentation for more details.

plot

signature(x = "Spectrum", y = "character"): Plots an MS2 level spectrum and its highlight the fragmention peaks. See plot.Spectrum.character documentation for more details.

quantify

signature(object = "Spectrum"): Quatifies defined peaks in the spectrum. See quantify documentation for more details.

removePeaks

signature(object = "Spectrum"): Remove peaks lower that a threshold t. See removePeaks documentation for more details and examples.

smooth

signature(x = "Spectrum"): Smooths spectrum. See smooth documentation for more details and examples.

show

signature(object = "Spectrum"): Displays object content as text.

trimMz

signature(object = "Spectrum"): Trims the MZ range of all the spectra of the MSnExp instance. See trimMz documentation for more details and examples.

isEmpty

signature(x = "Spectrum"): Checks if the x is an empty Spectrum.

as

signature(object = "Spectrum", "data.frame"): Coerces the Spectrum object to a two-column data.frame containing intensities and MZ values.

Note

This is a virtual class and can not be instanciated directly.

Author(s)

Laurent Gatto

See Also

Instaciable sub-classes "Spectrum1" and "Spectrum2" for MS1 and MS2 spectra.

lgatto/MSnbase documentation built on Nov. 12, 2024, 10:58 a.m.