\HeaderA{findPeaks-methods}{Feature detection for GC/MS and LC/MS Data - methods}{findPeaks.Rdash.methods}
\aliasA{findPeaks}{findPeaks-methods}{findPeaks}
\aliasA{findPeaks,xcmsRaw-method}{findPeaks-methods}{findPeaks,xcmsRaw.Rdash.method}
\keyword{methods}{findPeaks-methods}
\begin{Description}\relax
A number of peak pickers exist in XCMS. \code{findPeaks}
is the generic method.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] \code{\LinkA{xcmsRaw-class}{xcmsRaw.Rdash.class}} object
\item[\code{method}] Method to use for peak detection. See details.
\item[\code{...}] Optional arguments to be passed along
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Different algorithms can be used by specifying them with the
\code{method} argument. For example to use the matched filter
approach described by Smith et al (2006) one would use:
\code{findPeaks(object, method="matchedFilter")}. This is also
the default.

Further arguments given by \code{...} are
passed through to the function implementing
the \code{method}. 

A character vector of \emph{nicknames} for the 
algorithms available is returned by 
\code{getOption("BioC")\$xcms\$findPeaks.methods}.
If the nickname of a method is called "centWave",
the help page for that specific method can
be accessed with \code{?findPeaks.centWave}.
\end{Details}
\begin{Value}
A matrix with columns:
\begin{ldescription}
\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{rt}] retention time of peak midpoint

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

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

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

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

\end{ldescription}


and additional columns depending on the choosen method.
\end{Value}
\begin{Section}{Methods}
\describe{
\item[object = "xcmsRaw"] \code{
    findPeaks(object, ...)
  }

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

