removePeaks-methods {MSnbase} | R Documentation

## Removes low intensity peaks

### Description

This method sets low intensity peaks from individual spectra (`Spectrum` instances) or whole experiments (`MSnExp` instances) to 0. The intensity threshold is set with the `t` parameter. Default is the `"min"` character. The threshold is then set as the non-0 minimum intensity found in the spectrum. Any other numeric values is valid. All peaks with maximum intensity smaller or equal to `t` are set to 0.

If the spectrum is in profile mode, ranges of successive non-0 peaks <= `t` are set to 0. If the spectrum is centroided, then individual peaks <= `t` are set to 0. See the example below for an illustration.

Note that the number of peaks is not changed; the peaks below the threshold are set to 0 and the object is not cleanded out (see `clean`). An illustrative example is shown below.

### Methods

`signature(object = "MSnExp", t, verbose = "logical" )`

  Removes low intensity peaks of all spectra in `MSnExp` object. `t` sets the minimum peak intensity. Default is "min", i.e the smallest intensity in each spectrum. Other `numeric` values are valid. Displays a control bar if verbose set to `TRUE` (default). Returns a new `MSnExp` instance.

`signature(object = "Spectrum", t, msLevel. = "numeric")`

  Removes low intensity peaks of `Spectrum` object. `t` sets the minimum peak intensity. Default is "min", i.e the smallest intensity in each spectrum. Other `numeric` values are valid. `msLevel.` defines the level of the spectrum, and if `msLevel(object) != msLevel.`, cleaning is ignored. Only relevant when called from `OnDiskMSnExp` and is only relevant for developers.

  Returns a new `Spectrum` instance.

### Author(s)

Laurent Gatto <lg390@cam.ac.uk>

### See Also

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

### Examples

    int <- c(2, 0, 0, 0, 1, 5, 1, 0, 0, 1, 3, 1, 0, 0, 1, 4, 2, 1)
    sp1 <- new("Spectrum2",
               intensity = int,
               mz = 1:length(int),
               centroided = FALSE)
    sp2 <- removePeaks(sp1) ## no peaks are removed here
                            ## as min intensity is 1 and
                            ## no peak has a max int <= 1
    sp3 <- removePeaks(sp1, 3)
    intensity(sp1)
    intensity(sp2)
    intensity(sp3)

    peaksCount(sp1) == peaksCount(sp2)
    peaksCount(sp3) <= peaksCount(sp1)

    data(itraqdata)
    itraqdata2 <- removePeaks(itraqdata, t = 2.5e5)
    table(unlist(intensity(itraqdata)) == 0)
    table(unlist(intensity(itraqdata2)) == 0)
    processingData(itraqdata2)

    ## difference between centroided and profile peaks

    int <- c(104, 57, 32, 33, 118, 76, 38, 39, 52, 140, 52, 88, 394, 71,
             408, 94, 2032)
    sp <- new("Spectrum2",
              intensity = int,
              centroided = FALSE,
              mz = seq_len(length(int)))

    ## unchanged, as ranges of peaks <= 500 considered
    intensity(removePeaks(sp, 500))
    stopifnot(identical(intensity(sp), intensity(removePeaks(sp, 500))))

    centroided(sp) <- TRUE
    ## different!
    intensity(removePeaks(sp, 500))

[Package MSnbase version 2.12.0 Index]