\HeaderA{group-methods}{Group peaks from different samples together}{group.Rdash.methods}
\aliasA{group.nearest}{group-methods}{group.nearest}
\aliasA{group.nearest,xcmsSet-method}{group-methods}{group.nearest,xcmsSet.Rdash.method}
\keyword{methods}{group-methods}
\keyword{file}{group-methods}
\begin{Description}\relax
Group peaks together across samples by creating a master peak list and
assigning corresponding peaks from all samples. It is inspired by the
alignment algorithm of mzMine. For further details check
\url{http://mzmine.sourceforge.net/} and

Katajamaa M, Miettinen J, Oresic M: MZmine: Toolbox for processing and
visualization of mass spectrometry based molecular profile
data. Bioinformatics (Oxford, England) 2006, 22:634?636.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] the \code{xcmsSet} object
\item[\code{mzVsRTbalance}] Multiplicator for mz value before calculating the
(euclidean) distance between two peaks.
\item[\code{mzCheck}] Maximum tolerated distance for mz.
\item[\code{rtCheck}] Maximum tolerated distance for RT.
\item[\code{rtCheck}] Number of nearest Neighbours to check
\end{ldescription}
\end{Arguments}
\begin{Value}
An \code{xcmsSet} object with peak group assignments and statistics.
\end{Value}
\begin{Section}{Methods}
\describe{
\item[object = "xcmsSet"] \code{    
    group(object, mzVsRTbalance=10, mzCheck=0.2, rtCheck=15, kNN=10)
  }

}
\end{Section}
\begin{SeeAlso}\relax
\code{\LinkA{xcmsSet-class}{xcmsSet.Rdash.class}},
\code{\LinkA{group.density}{group.density}} and 
\code{\LinkA{group.mzClust}{group.mzClust}}
\end{SeeAlso}

