annotate-methods: Automatic deconvolution/annotation of LC/ESI-MS data

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

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 <[e-mail]>

Examples

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

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