\HeaderA{groupval-methods}{Extract a matrix of peak values for each group}{groupval.Rdash.methods}
\aliasA{groupval}{groupval-methods}{groupval}
\aliasA{groupval,xcmsSet-method}{groupval-methods}{groupval,xcmsSet.Rdash.method}
\keyword{methods}{groupval-methods}
\keyword{manip}{groupval-methods}
\begin{Description}\relax
Generate a matrix of peak values with rows for every group and
columns for every sample. The value included in the matrix can
be any of the columns from the \code{xcmsSet} \code{peaks} slot
matrix. Collisions where more than one peak from a single sample
are in the same group get resolved with one of several user-selectable
methods.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] the \code{xcmsSet} object
\item[\code{method}] conflict resolution method, \code{"medret"} to use the peak
closest to the median retention time or \code{"maxint"} to use
the peak with the highest intensity

\item[\code{value}] name of peak column to enter into returned matrix, or \code{"index"}
for index to the corresponding row in the \code{peaks} slot
matrix

\item[\code{intensity}] if \code{method == "maxint"}, name of peak column to use for
intensity

\end{ldescription}
\end{Arguments}
\begin{Value}
A matrix with with rows for every group and columns for every
sample. Missing peaks have \code{NA} values.
\end{Value}
\begin{Section}{Methods}
\describe{
\item[object = "xcmsSet"] \code{groupval(object, method = c("medret", "maxint"),
                 value = "index", intensity = "into")}

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

