\name{xsAnnotate-class}
\docType{class}
\alias{xsAnnotate-class}
\alias{show,xsAnnotate-method}
\title{Class xsAnnotate, a class for annotate peak data}
\description{
  This class transforms a set of peaks from multiple LC/MS or GC/MS
  samples into a matrix of preprocessed data. It groups the peaks
  and does nonlinear retention time correction without internal
  standards. It fills in missing peak values from raw data. Lastly,
  it generates extracted ion chromatograms for ions of interest.
}
\section{Objects from the Class}{
  Objects can be created with the \code{\link{xsAnnotate}} constructor
  which gathers peaks from a set NetCDF files. Objects can also be
  created by calls of the form \code{new("xsAnnotate", ...)}.
}

%Slots for class 'xsAnnotate'
%  Code: annoGrp annoID derivativeIons formula isoID groupInfo
%        isotopes polarity pspectra psSamples ruleset runParallel sample xcmsSet

\section{Slots}{
  \describe{
    \item{\code{annoGrp}:}{Assignment of mass hypotheses to correlation groups}
    \item{\code{annoID}:}{The assignemnt of peaks to the mass difference rule used}
    \item{\code{derivativeIons}:}{List with annotation result for every peak}
    \item{\code{formula}:}{Matrix containing putative sum formula (intended for future use)}
    \item{\code{isoID}:}{Matrix containing IDs and additional of all annotated isotope peaks}
    \item{\code{groupInfo}:}{(grouped) Peaktable with "into" values}
    \item{\code{isotopes}:}{List with annotated isotopid results for every peak}
    \item{\code{polarity}:}{A single string with the polarity mode of the peaks}
    \item{\code{pspectra}:}{List contains all pseudospectra with there peak IDs}
    \item{\code{psSamples}:}{List containing information with sample was sample was selecteted as representative (automatic selection)}
    \item{\code{ruleset}:}{A dataframe describing the mass difference rules used for the annotion}
    \item{\code{runParallel}:}{Flag if CAMERA runs in serial or parallel mode}
    \item{\code{sample}:}{Number of the used xcmsSet sample (beforehand sample selection)}
    \item{\code{xcmsSet}:}{The embedded xcmsSet}
  }
}

\section{Methods}{
  \describe{
    \item{\link{groupFWHM}}{
      \code{signature(object = "xsAnnotate")}: group the peak data after the FWHM of the retention time
    }
    \item{\link{groupCorr}}{
      \code{signature(object = "xsAnnotate")}: group the peak data after the correlation of the EICs
    }
    \item{\link{findIsotopes}}{
      \code{signature(object = "xsAnnotate")}: search for possible isotopes in the spectra
    }
    \item{\link{findAdducts}}{
      \code{signature(object = "xsAnnotate")}: search for possible adducts in the spectra
    }
    \item{\link{plotEICs}}{
      \code{signature(object = "xsAnnotate")}: plot EICs of pseudospectra 
    }
  }
}
\author{Carsten Kuhl, \email{ckuhl@ipb-halle.de}}
\note{
  No notes yet.
}
\seealso{
  \code{\link{xsAnnotate}}
}
\keyword{classes}