getPeaklist-methods: Generate the annotatad peaklist

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

Generate the annotatad peaklist

Description

Extract all information from an xsAnnotate object. Returns a peaklist with annotated peaks.

Usage

  getPeaklist(object, intval="into")

Arguments

object	xsAnnotate object
intval	Choose intensity values. Allowed values are into, maxo, intb, intf, maxf, area, depending on the feature detection algorithm used.

Details

This function extract the peaktable from an xsAnnotate object, containing three additional columns (isotopes, adducts, pseudospectrum) with represents the annotation results. For a grouped xcmsSet it returns the grouped peaktable.

Author(s)

Carsten Kuhl <[e-mail]>

Examples

library(CAMERA)
file <- system.file('mzML/MM14.mzML', package = "CAMERA")
xs   <- xcmsSet(file, method="centWave", ppm=30, peakwidth=c(5,10))
an   <- xsAnnotate(xs)
an   <- groupFWHM(an)
an   <- findIsotopes(an)
an   <- findAdducts(an,polarity="positive")
peaklist <- getPeaklist(an)

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