navMS: Navigate an 'MSnExp' object

In lgatto/MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

Navigate an MSnExp object

Description

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(s)

Laurent Gatto

Examples

f <- msdata::proteomics(full.names = TRUE, pattern = "MS3")
x <- readMSData(f, centroided. = c(FALSE, TRUE, FALSE), mode = "onDisk")
(sp <- which(msLevel(x) == 3)[2]) ## 2nd MS3 spectrum
x[[sp]] ## curent MS3
MSnbase:::nextMS(sp, x) ## next MS3
MSnbase:::prevMS(sp, x) ## prev MS3
MSnbase:::prevMS(sp, x, 2L) ## prev MS2
MSnbase:::prevMS(sp, x, 1L) ## prev MS1

lgatto/MSnbase documentation built on March 14, 2024, 7:06 a.m.