Navigate an MSnExp object — navMS • MSnbase

Navigate an MSnExp object by moving to the next or previous spectrum.

Usage

navMS(i, object, msLevel, nav = c("nextMS", "prevMS"), ...)

nextMS(...)

prevMS(...)

Arguments

i: The name or index of the current spectrum
object: The MSnExp object
msLevel: The MS level of the next or previous spectrum. If missing (default), then the level of the current spectrum is used.
nav: One of "nextMS" or "prevMS", to obtain the next or previous spectrum of level msLevel.
...: Additional parameters. Currently ignored.

Value

An object of class Spectrum1 or Spectrum2, depending on the value of msLevel or NULL, of no spectrum is found.

Author

Laurent Gatto

Examples

f <- msdata::proteomics(full.names = TRUE, pattern = "MS3")
x <- readMSData(f, centroided. = c(FALSE, TRUE, FALSE), mode = "onDisk")
#> Warning: Reading different file formats in.
#> This is untested and you are welcome to try it out.
#> Please report back!
(sp <- which(msLevel(x) == 3)[2]) ## 2nd MS3 spectrum
#> F1.S009 
#>       9 
x[[sp]] ## curent MS3
#> Object of class "Spectrum2"
#>  Precursor: 756.4332 
#>  Retention time: 73:43 
#>  Charge: 1 
#>  MSn level: 3 
#>  Peaks count: 1422 
#>  Total ion count: 972514 
MSnbase:::nextMS(sp, x) ## next MS3
#> Object of class "Spectrum2"
#>  Precursor: 466.1647 
#>  Retention time: 73:44 
#>  Charge: 0 
#>  MSn level: 3 
#>  Peaks count: 2281 
#>  Total ion count: 3908748 
MSnbase:::prevMS(sp, x) ## prev MS3
#> Object of class "Spectrum2"
#>  Precursor: 490.2629 
#>  Retention time: 73:43 
#>  Charge: 0 
#>  MSn level: 3 
#>  Peaks count: 2540 
#>  Total ion count: 9311294 
MSnbase:::prevMS(sp, x, 2L) ## prev MS2
#> Object of class "Spectrum2"
#>  Precursor: 675.6938 
#>  Retention time: 73:43 
#>  Charge: 3 
#>  MSn level: 2 
#>  Peaks count: 858 
#>  Total ion count: 627600.3 
MSnbase:::prevMS(sp, x, 1L) ## prev MS1
#> Object of class "Spectrum1"
#>  Retention time: 73:43 
#>  MSn level: 1 
#>  Total ion count: 48304 
#>  Polarity: 1