ESI-MS data
In CAMERA: Collection of annotation related methods for mass spectrometry data

Description Usage Arguments Details Value Author(s) Examples

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

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")

`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)

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.

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

Carsten Kuhl <ckuhl@ipb-halle.de>

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