\HeaderA{fillPeaks-methods}{Integrate areas of missing peaks}{fillPeaks.Rdash.methods}
\aliasA{fillPeaks}{fillPeaks-methods}{fillPeaks}
\aliasA{fillPeaks,xcmsSet-method}{fillPeaks-methods}{fillPeaks,xcmsSet.Rdash.method}
\keyword{methods}{fillPeaks-methods}
\keyword{file}{fillPeaks-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
\item[\code{method}] the filling method
\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. According to the type of raw-data there are 2 different 
methods available. for filling gcms/lcms data the method "chrom" integrates 
raw-data in the chromatographic domain, whereas "MSW" is used for  
peaklists without retention-time information like those from 
direct-infusion spectra.
\end{Details}
\begin{Value}
A \code{xcmsSet} objects with filled in peak groups.
\end{Value}
\begin{Section}{Methods}
\describe{
\item[object = "xcmsSet"] \code{fillPeaks(object, method="")}

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

