\name{getIsotopeCluster}
\alias{getIsotopeCluster}
\title{Retrieve the annotatad isotopes}
\description{
 Extract all annotated isotope cluster. Returns a list with one element per cluster.
 A element contains the charge of the molecule and a peakmatrix with mz and intensity value.
}
\usage{
  getIsotopeCluster(object, number=NULL, value="maxo")
}
\arguments{
  \item{object}{ xsAnnotate object}
  \item{number}{ Set to NULL extract all isotope cluster or to specific choosen ones }
  \item{value}{ Which intensity values should be extracted. Allowed values are: maxo, into, intb}
}
\details{
  This method extract the isotope annotation from a xsAnnotate object. The order of the resulting list is the same as the one in the peaklist, see \code{\link{getPeaklist}}.
  In the case of a multiple sample the intensity value for a peak is retrieved from the sample, which has been choosen for the pseudospectra in the grouping step. 
}
\examples{
  #single sample
  library(CAMERA)
  file <- system.file('mzdata/MM14.mzdata', package = "CAMERA")
  xs   <- xcmsSet(file, method="centWave", ppm=30, peakwidth=c(5,10))
  an   <- xsAnnotate(xs)
  an   <- groupFWHM(an)
  an   <- findIsotopes(an) 
  isolist <- getIsotopeCluster(an)
  isolist[[10]] #get IsotopeCluster 10

  #multiple sample
  library(faahKO)
  xs <- group(faahko)
  xs <- fillPeaks(xs)
  an   <- xsAnnotate(xs)
  an   <- groupFWHM(an)
  an   <- findIsotopes(an) 
  isolist <- getIsotopeCluster(an)

  ##Interaction with Rdisop
 \dontrun{
  library(Rdisop)
  isotopes.decomposed <- lapply(isolist,function(x) {
    decomposeIsotopes(x$peaks[,1],x$peaks[,2],z=x$charge);
  }) #decomposed isotope cluster, filter steps are recommended
 }
}
\author{Carsten Kuhl <ckuhl@ipb-halle.de>}
\keyword{methods}