\HeaderA{xcmsEIC-class}{Class xcmsEIC, a class for multi-sample extracted ion chromatograms}{xcmsEIC.Rdash.class}
\aliasA{mzrange}{xcmsEIC-class}{mzrange}
\aliasA{mzrange,xcmsEIC-method}{xcmsEIC-class}{mzrange,xcmsEIC.Rdash.method}
\aliasA{rtrange}{xcmsEIC-class}{rtrange}
\aliasA{rtrange,xcmsEIC-method}{xcmsEIC-class}{rtrange,xcmsEIC.Rdash.method}
\aliasA{show,xcmsEIC-method}{xcmsEIC-class}{show,xcmsEIC.Rdash.method}
\keyword{classes}{xcmsEIC-class}
\begin{Description}\relax
This class is used to store and plot parallel extracted ion
chromatograms from multiple sample files. It integrates with the
\code{xcmsSet} class to display peak area integrated during peak
identification or fill-in.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created with the \code{\LinkA{getEIC}{getEIC}} method of
the \code{xcmsSet} class. Objects can also be created by calls
of the form \code{new("xcmsEIC", ...)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{eic}:] list containing named entries for every sample. for each entry, a 
list of two column EIC matricies with retention time and intensity

\item[\code{mzrange}:] two column matrix containing starting and ending m/z for each EIC

\item[\code{rtrange}:] two column matrix containing starting and ending time for
each EIC

\item[\code{rt}:] either \code{"raw"} or \code{"corrected"} to specify retention
times contained in the object

\item[\code{groupnames}:] group names from \code{xcmsSet} object used to generate EICs

}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[\LinkA{groupnames}{groupnames}] \code{signature(object = "xcmsEIC")}: get \code{groupnames} slot

\item[mzrange] \code{signature(object = "xcmsEIC")}: get \code{mzrange} slot

\item[\LinkA{plot}{plot}] \code{signature(x = "xcmsEIC")}: plot the extracted ion
chromatograms

\item[rtrange] \code{signature(object = "xcmsEIC")}: get \code{rtrange} slot

\item[\LinkA{sampnames}{sampnames}] \code{signature(object = "xcmsEIC")}: get sample names

}
\end{Section}
\begin{Note}\relax
No notes yet.
\end{Note}
\begin{Author}\relax
Colin A. Smith, \email{csmith@scripps.edu}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{getEIC}{getEIC}}
\end{SeeAlso}

