MSnbase: removePeaks-methods – R documentation

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removePeaks-methods

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>

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))

MSnbase

Base Functions and Classes for Mass Spectrometry and Proteomics

v2.16.1

Artistic-2.0

Authors

Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker and Lieven Clement.

Initial release