\HeaderA{xcmsFragments-class}{Class xcmsFragments, a class for handling Tandem MS and MS$\textasciicircum{}n$ data}{xcmsFragments.Rdash.class}
\aliasA{plotTree}{xcmsFragments-class}{plotTree}
\aliasA{plotTree,xcmsFragments-method}{xcmsFragments-class}{plotTree,xcmsFragments.Rdash.method}
\aliasA{show,xcmsFragments-method}{xcmsFragments-class}{show,xcmsFragments.Rdash.method}
\keyword{classes}{xcmsFragments-class}
\begin{Description}\relax
This class is similar to \code{\LinkA{xcmsSet}{xcmsSet}} because it stores peaks
from a number of individual files. However,  xcmsFragments keeps
Tandem MS and e.g. Ion Trap or Orbitrap MS$\textasciicircum{}n$ peaks, including the
parent ion relationships.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created with the \code{\LinkA{xcmsFragments}{xcmsFragments}}
constructor and filled with peaks using the collect method.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{peaks}:] matrix with colmns peakID (MS1 parent in corresponding xcmsSet),
MSnParentPeakID (parent peak within this xcmsFragments), msLevel
(e.g. 2 for Tandem MS), rt (retention time in case of LC data), mz
(fragment mass-to-charge), intensity (peak intensity as reported
by XXX), sample (The ID of the rawData-file).

}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[\LinkA{collect}{collect}] \code{signature(object = "xcmsFragments")}: gets a xcmsSet-object, collects ms1-peaks from it and the msn-peaks from the corresponding xcmsRaw-files.

\item[plotTree] \code{signature(object = "xcmsFragments")}: prints a (text based) pseudo-tree of the peaktable to display the dependencies of the peaks among each other.

\item[\LinkA{show}{show}] \code{signature(object = "xcmsFragments")}: print a human-readable
description of this object to the console.

}
\end{Section}
\begin{Note}\relax
No notes yet.
\end{Note}
\begin{Author}\relax
S. Neumann, J. Kutzera
\end{Author}
\begin{References}\relax
A parallel effort in metabolite profiling data sharing:
\url{http://metlin.scripps.edu/}
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{xcmsRaw}{xcmsRaw}}
\end{SeeAlso}

