\HeaderA{xsAnnotate-class}{Class xsAnnotate, a class for annotate peak data}{xsAnnotate.Rdash.class}
\aliasA{show,xsAnnotate-method}{xsAnnotate-class}{show,xsAnnotate.Rdash.method}
\keyword{classes}{xsAnnotate-class}
\begin{Description}\relax
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.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created with the \code{\LinkA{xsAnnotate}{xsAnnotate}} constructor
which gathers peaks from a set NetCDF files. Objects can also be
created by calls of the form \code{new("xsAnnotate", ...)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{peaks}:] matrix containing peak data

\item[\code{pspectra}:] list containing peak data

\item[\code{isotopes}:] matrix containing peak data

\item[\code{derivativeIons}:] matrix containing peak data

\item[\code{formula}:] matrix containing peak data

\item[\code{sample}:] the number of the used xcmsSet sample

}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[\LinkA{groupFWHM}{groupFWHM}] \code{signature(object = "xsAnnotate")}: group the peak data after the FWHM of the retention time

\item[\LinkA{groupCorr}{groupCorr}] \code{signature(object = "xsAnnotate")}: group the peak data after the Correlation of the EIC

\item[\LinkA{findIsotopes}{findIsotopes}] \code{signature(object = "xsAnnotate")}: search for possible isotopes in the spectra

\item[\LinkA{findAdducts}{findAdducts}] \code{signature(object = "xsAnnotate")}: search for possible adducts in the spectra

}
\end{Section}
\begin{Note}\relax
No notes yet.
\end{Note}
\begin{Author}\relax
Carsten Kuhl, \email{ckuhl@ipb-halle.de}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{xsAnnotate}{xsAnnotate}}
\end{SeeAlso}

