annotate-methods {CAMERA} | R Documentation

## Automatic deconvolution/annotation of LC/ESI-MS data

### Description

Wrapper skript for automatic annotation of isotope peaks, adducts and fragments for a (grouped) xcmsSet `xs`. The function returns an xsAnnotate object.

### Usage

    annotate(object, sample=NA, nSlaves=1, sigma=6, perfwhm=0.6,
      cor_eic_th=0.75, graphMethod="hcs", pval=0.05, calcCiS=TRUE,
      calcIso=FALSE, calcCaS=FALSE, maxcharge=3, maxiso=4, minfrac=0.5,
      ppm=5, mzabs=0.015, quick=FALSE, psg_list=NULL, rules=NULL,
      polarity="positive", multiplier=3, max_peaks=100 ,intval="into")

### Arguments

`object` | xcmsSet with peak group assignments
`sample` | xsAnnotate: Sample selection for grouped xcmsSet, see xsAnnotate-class
`nSlaves` | xsAnnotate: Use parallel CAMERA mode, require Rmpi
`sigma` | groupFWHM: multiplier of the standard deviation
`perfwhm` | groupFWHM: percentage of FWHM width
`cor_eic_th` | groupCorr: correlation threshold (0..1)
`graphMethod` | groupCorr: Method selection for grouping peaks after correlation analysis into pseudospectra
`pval` | groupCorr: significant correlation threshold
`calcCiS` | groupCorr: Use correlation inside samples for peak grouping
`calcIso` | groupCorr: Use isotopic relationship for peak grouping
`calcCaS` | groupCorr: Use correlation across samples for peak grouping
`maxcharge` | findIsotopes: max. ion charge
`maxiso` | findIsotopes: max. number of expected isotopes
`minfrac` | findIsotopes: The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation
`ppm` | General ppm error
`mzabs` | General absolut error in m/z
`quick` | Use only groupFWHM and findIsotopes
`psg_list` | Calculation will only be done for the selected groups
`rules` | findAdducts: User defined ruleset
`polarity` | findAdducts: Which polarity mode was used for measuring of the ms sample
`multiplier` | findAdducts: If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions
`max_peaks` | How much peaks will be calculated in every thread using the parallel mode
`intval` | General used intensity value (into, maxo, intb)

### Details

Batch script for annotation of an (grouped) xcmsSet `xs`. Generates an xsAnnotate object by calling all involved functions for the annotation step. Function list: 1: groupFWHM() , 2: findIsotopes() , 3: groupCorr(), 4: findAdducts() Return the xsAnnotate object, which inherits all annotations. For more information about the parameters see the specific function manpages.

### Value

`annotate` returns an xsAnnotate object. For more information about the xsAnnotate object 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))
     xsa  <- annotate(xs)

[Package CAMERA version 1.40.0 Index]