\HeaderA{group-methods}{Group peaks from different samples together}{group.Rdash.methods}
\aliasA{group}{group-methods}{group}
\aliasA{group,xcmsSet-method}{group-methods}{group,xcmsSet.Rdash.method}
\keyword{methods}{group-methods}
\begin{Description}\relax
A number of grouping (or alignment) methods exist in XCMS. \code{group}
is the generic method.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] \code{\LinkA{xcmsSet-class}{xcmsSet.Rdash.class}} object
\item[\code{method}] Method to use for grouping. See details.
\item[\code{...}] Optional arguments to be passed along
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Different algorithms can be used by specifying them with the
\code{method} argument. For example to use the density-based 
approach described by Smith et al (2006) one would use:
\code{group(object, method="density")}. This is also the default.

Further arguments given by \code{...} are
passed through to the function implementing
the \code{method}. 

A character vector of \emph{nicknames} for the 
algorithms available is returned by 
\code{getOption("BioC")\$xcms\$group.methods}.
If the nickname of a method is called "mzClust",
the help page for that specific method can
be accessed with \code{?group.mzClust}.
\end{Details}
\begin{Value}
An \code{xcmsSet} object with peak group assignments and statistics.
\end{Value}
\begin{Section}{Methods}
\describe{
\item[object = "xcmsSet"] \code{
    group(object, ...)
  }

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

