CAMERA (version 1.28.0)

annotate-methods: 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)

Value

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

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.

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)