\HeaderA{getPeaks-methods}{Get peak intensities for specified regions}{getPeaks.Rdash.methods}
\aliasA{getPeaks}{getPeaks-methods}{getPeaks}
\aliasA{getPeaks,xcmsRaw-method}{getPeaks-methods}{getPeaks,xcmsRaw.Rdash.method}
\keyword{methods}{getPeaks-methods}
\keyword{manip}{getPeaks-methods}
\begin{Description}\relax
Integrate extracted ion chromatograms in pre-defined defined
regions. Return output similar to \code{\LinkA{findPeaks}{findPeaks}}.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] the \code{xcmsSet} object
\item[\code{peakrange}] matrix or data frame with 4 columns: \code{mzmin}, \code{mzmax},
\code{rtmin}, \code{rtmax} (they must be in that order or named)

\item[\code{step}] step size to use for profile generation
\end{ldescription}
\end{Arguments}
\begin{Value}
A matrix with columns:
\begin{ldescription}
\item[\code{i}] rank of peak identified in merged EIC (\textless{}= \code{max}), always \code{NA}

\item[\code{mz}] weighted (by intensity) mean of peak m/z across scans

\item[\code{mzmin}] m/z of minimum step

\item[\code{mzmax}] m/z of maximum step

\item[\code{ret}] retention time of peak midpoint

\item[\code{retmin}] leading edge of peak retention time

\item[\code{retmax}] trailing edge of peak retention time

\item[\code{into}] integrated area of original (raw) peak

\item[\code{intf}] integrated area of filtered peak, always \code{NA}

\item[\code{maxo}] maximum intensity of original (raw) peak

\item[\code{maxf}] maximum intensity of filtered peak, always \code{NA}

\end{ldescription}
\end{Value}
\begin{Section}{Methods}
\describe{
\item[object = "xcmsRaw"] \code{getPeaks(object, peakrange, step = 0.1)}

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

