annotate {CAMERA}R Documentation

Deconvolute/Annotate LC/ESI-MS data

Description

Annotate isotope peaks, adducts and fragments for a (grouped) xcmsSet xs. Returns a xsAnnotate object.

Usage

annotate(xs, sigma = 6, perfwhm = 0.6, cor_eic_th = 0.75, maxcharge = 3, maxiso = 4, ppm = 5, mzabs = 0.01, multiplier = 3, sample=1, category = NA, polarity="positive")

Arguments

xs xcmsSet with peak group assignments
sigma Isotopic peak relationship table
perfwhm Adduct/Fragment peak relationship table
cor_eic_th correlation threshold (0..1)
maxcharge max charge of the ions
maxiso max number of isotopes
ppm ppm error
mzabs absolut error
multiplier max. number n of [nM+x] clusterions
sample Index of which sample is used for the correlation
category Which class label should be used
polarity Which polarity mode was used for measuring of the ms sample

Details

Batch script for a annotation for a a (grouped) xcmsSet xs. Generate intern a xsAnnotate object and calls the member function for the annotation step. Returns a peaklist with additonal columns for isotopes, adducts and an index for the pseudo spectra group. xsAnnotate groups Peaks into spectra groups, after there Retentiontime and EIC correlations. Attention: For the EIC correlation only one sample can be used, so if the xcmsSet contains more than one sample, one must be chosen.

Value

annotate returns an xsAnnotate object. For more information about see xsAnnotate-class

Author(s)

Carsten Kuhl <ckuhl@ipb-halle.de>

Examples

 library(CAMERA)
 file <- system.file('mzdata/MM14.mzdata', package = "CAMERA")
 xs   <- xcmsSet(file, method="centWave", ppm=30, peakwidth=c(5,10))
 annotated_xs<- annotate(xs)

[Package CAMERA version 1.0.0 Index]