removeReporters-methods {MSnbase} | R Documentation

## Removes reporter ion tag peaks

### Description

This methods sets all the reporter tag ion peaks from one MS2 spectrum or all the MS2 spectra of an experiment to 0. Reporter data is specified using an `"ReporterIons"` instance. The peaks are selected around the expected reporter ion m/z value +/- the reporter width. Optionally, the spectrum/spectra can be `cleaned` to remove successive 0 intensity data points (see the `clean` function for details).

Note that this method only works for MS2 spectra or experiments that contain MS2 spectra. It will fail for MS1 spectrum.

### Methods

`signature(object = "MSnExp", reporters = "ReporterIons", clean = "logical", verbose = "logical" )`

  The reporter ion peaks defined in the `reporters` instance of all the MS2 spectra of the `"MSnExp"` instance are set to 0 and, if `clean` is set to `TRUE`, cleaned. The default value of `reporters` is `NULL`, which leaves the spectra as unchanged. The `verbose` parameter (default is `TRUE`) defines whether a progress bar should be showed.

`signature(object = "Spectrum", reporters = "ReporterIons", clean = "FALSE")`

  The reporter ion peaks defined in the `reporters` instance of MS2 `"Spectrum"` instance are set to 0 and, if `clean` is set to `TRUE`, cleaned. The default value of `reporters` is `NULL`, which leaves the spectrum as unchanged.

### Author(s)

Laurent Gatto <lg390@cam.ac.uk>

### See Also

`clean` and `removePeaks` for other spectra processing methods.

### Examples

    sp1 <- itraqdata[[1]]
    sp2 <- removeReporters(sp1,reporters=iTRAQ4)
    sel <- mz(sp1) > 114 & mz(sp1) < 114.2
    mz(sp1)[sel]
    intensity(sp1)[sel]
    plot(sp1,full=TRUE,reporters=iTRAQ4)
    intensity(sp2)[sel]
    plot(sp2,full=TRUE,reporters=iTRAQ4)

[Package MSnbase version 2.12.0 Index]