\HeaderA{fillPeaks.MSW-methods}{Integrate areas of missing peaks in FTICR-MS data}{fillPeaks.MSW.Rdash.methods}
\aliasA{fillPeaks.MSW}{fillPeaks.MSW-methods}{fillPeaks.MSW}
\aliasA{fillPeaks.MSW,xcmsSet-method}{fillPeaks.MSW-methods}{fillPeaks.MSW,xcmsSet.Rdash.method}
\keyword{methods}{fillPeaks.MSW-methods}
\keyword{file}{fillPeaks.MSW-methods}
\begin{Description}\relax
For each sample, identify peak groups where that sample is not
represented. For each of those peak groups, integrate the signal
in the region of that peak group and create a new peak.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] the \code{xcmsSet} object
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
After peak grouping, there will always be peak groups that do not
include peaks from every sample. This method produces intensity
values for those missing samples by integrating raw data in peak
group region. In a given group, the start and ending m/z values for 
integration are defined by the median start and
end points of the other detected peaks.
\end{Details}
\begin{Value}
A \code{xcmsSet} objects with filled in peak groups.
\end{Value}
\begin{Section}{Methods}
\describe{
\item[object = "xcmsSet"] \code{fillPeaks.MSW(object)}

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

