Trims 'MSnExp' or 'Spectrum' instances

This method selects a range of MZ values in a single spectrum (Spectrum instances) or all the spectra of an experiment (MSnExp instances). The regions to trim are defined by the range of mz argument, such that MZ values <= min(mz) and MZ values >= max(mz) are trimmed away.

Methods

signature(object = "MSnExp", mz = "numeric", msLevel. = "numeric")

Trims all spectra in MSnExp object according to mz. If msLevel. is defined, then only spectra of that level are trimmer.

signature(object = "Spectrum", mz = "numeric", msLevel. = "numeric")

Trims the Spectrum object and retruns a new trimmed object. 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.

Author

Laurent Gatto

See also

removePeaks and clean for other spectra processing methods.

Examples

mz <- 1:100
sp1 <- new("Spectrum2",
           mz = mz,
           intensity = abs(rnorm(length(mz))))

sp2 <- trimMz(sp1, c(25, 75))
range(mz(sp1))
#> [1]   1 100
range(mz(sp2))
#> [1] 25 75

data(itraqdata)
itraqdata2 <- filterMz(itraqdata, c(113, 117))
range(mz(itraqdata))
#> [1]   99.99872 2069.27344
range(mz(itraqdata2))
#> [1] 113.0459 116.7362
processingData(itraqdata2)
#> - - - Processing information - - -
#> Data loaded: Wed May 11 18:54:39 2011 
#> Updated from version 0.3.0 to 0.3.1 [Fri Jul  8 20:23:25 2016] 
#> Filter: trim MZ [113..117] on MS level(s) 2. 
#>  MSnbase version: 1.1.22