getpspectra: Retrieve a peaklist of one or more pseudospectra

In sneumann/CAMERA: Collection of annotation related methods for mass spectrometry data

Retrieve a peaklist of one or more pseudospectra

Description

Extract group(s) from a xsAnnotate object. Returns a peaklist as matrix with annotated peaks.

Usage

  getpspectra(object, grp)

Arguments

object	xsAnnotate object
grp	index of pseudo-spectra-group

Details

xsAnnotate groups LC/MS Peaklist after there EIC correlation and FWHM. These function extract one or more of these so called "pseudo spectra groups" with include the peaklist with there annotations. The annotation depends on a before called findAdducts() ( and findIsotopes() ). Important: The indices for the isotopes, are those from the whole peaklist. See getPeaklist().

Author(s)

Carsten Kuhl <[e-mail]>

Examples

  library(CAMERA)
  file <- system.file('mzML/MM14.mzML', package = "CAMERA")
  xs   <- xcmsSet(c(file), method="centWave", ppm=30, peakwidth=c(5,10))
  an   <- xsAnnotate(xs)
  an   <- groupFWHM(an)
  #For one group
  peaklist <- getpspectra(an, 1)
  #For two groups
  peaklist <- getpspectra(an, c(1,2))

sneumann/CAMERA documentation built on April 5, 2024, 2:33 a.m.