Spectrum-class {MSnbase} | R Documentation

## 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 `qtl`th 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(object1 = "Spectrum", object2 = "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 <lg390@cam.ac.uk>

### See Also

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

[Package MSnbase version 2.15.7 Index]