clean-methods.RdThis method cleans out individual spectra (Spectrum instances),
chromatograms (Chromatogram instances)
or whole experiments (MSnExp instances) of 0-intensity
peaks. Unless all is set to FALSE, original 0-intensity
values are retained only around peaks. If more than two 0's were
separating two peaks, only the first and last ones, those directly
adjacent to the peak ranges are kept. If two peaks are separated by
only one 0-intensity value, it is retained. An illustrative example is
shown below.
signature(object = "MSnExp", all = "logical", verbose =
"logical")Cleans all spectra in MSnExp
object. Displays a control bar if verbose set to TRUE
(default). Returns a cleaned MSnExp instance.
signature(object = "Spectrum", all = "logical",
msLevel. = "numeric")Cleans the Spectrum
object. Returns a cleaned Spectrum instance. If all
= TRUE, then all zeros are removed. 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.
signature(object = "Chromatogram", all = "logical",
na.rm = "logical")Cleans the Chromatogram instance and returns
a cleaned Chromatogram object. If
na.rm is TRUE (default is FALSE) all
NA intensities are removed before cleaning the chromatogram.
removePeaks and trimMz for other spectra
processing methods.
int <- c(1,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0)
sp1 <- new("Spectrum2",
intensity=int,
mz=1:length(int))
sp2 <- clean(sp1) ## default is all=FALSE
intensity(sp1)
#> [1] 1 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0
intensity(sp2)
#> [1] 1 0 0 1 1 1 0 0 1 1 0 0 1 0
intensity(clean(sp1, all = TRUE))
#> [1] 1 1 1 1 1 1 1
mz(sp1)
#> [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
#> [26] 26 27 28 29 30 31 32
mz(sp2)
#> [1] 1 2 8 9 10 11 12 16 17 18 19 28 29 30
mz(clean(sp1, all = TRUE))
#> [1] 1 9 10 11 17 18 29
data(itraqdata)
itraqdata2 <- clean(itraqdata)
sum(peaksCount(itraqdata))
#> [1] 106289
sum(peaksCount(itraqdata2))
#> [1] 59747
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]
#> Spectra cleaned: Thu Mar 14 06:10:41 2024
#> MSnbase version: 1.1.22
## Create a simple Chromatogram object
chr <- Chromatogram(rtime = 1:12,
intensity = c(0, 0, 20, 0, 0, 0, 123, 124343, 3432, 0, 0, 0))
## Remove 0-intensity values keeping those adjacent to peaks
chr <- clean(chr)
intensity(chr)
#> [1] 0 20 0 0 123 124343 3432 0
## Remove all 0-intensity values
chr <- clean(chr, all = TRUE)
intensity(chr)
#> [1] 20 123 124343 3432
## Clean a Chromatogram with NAs.
chr <- Chromatogram(rtime = 1:12,
intensity = c(0, 0, 20, NA, NA, 0, 123, 124343, 3432, 0, 0, 0))
chr <- clean(chr, all = FALSE, na.rm = TRUE)
intensity(chr)
#> [1] 0 20 0 123 124343 3432 0