\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}
\keyword{file}{group-methods}
\begin{Description}\relax
Group peaks together across samples using overlapping m/z bins and
calculation of smoothed peak distributions in chromatographic time.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] the \code{xcmsSet} object
\item[\code{minfrac}] minimum fraction of samples necessary in at least one of the sample
groups for it to be a valid group

\item[\code{minsamp}] minimum number of samples necessary in at least one of the sample
groups for it to be a valid group

\item[\code{bw}] bandwidth (standard deviation or half width at half maximum)
of gaussian smoothing kernel to apply to the peak density
chromatogram

\item[\code{mzwid}] width of overlapping m/z slices to use for creating peak density
chromatograms and grouping peaks across samples

\item[\code{max}] maximum number of groups to identify in a single m/z slice

\item[\code{sleep}] seconds to pause between plotting successive steps of the peak
grouping algorithm. peaks are plotted as points showing relative
intensity. identified groups are flanked by dotted vertical
lines.

\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, bw = 30, minfrac = 0.5, minsamp = 1, 
    mzwid = 0.25, max = 5, sleep = 0)
  }

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

