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]