\HeaderA{findPeaks.MSW-methods}{Feature detection for single-spectrum non-chromatography MS data}{findPeaks.MSW.Rdash.methods}
\aliasA{findPeaks.MSW}{findPeaks.MSW-methods}{findPeaks.MSW}
\aliasA{findPeaks.MSW,xcmsRaw-method}{findPeaks.MSW-methods}{findPeaks.MSW,xcmsRaw.Rdash.method}
\keyword{methods}{findPeaks.MSW-methods}
\begin{Description}\relax
Processing Mass Spectrometry direct-injection
spectrum by using wavelet based algorithm.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] \code{xcmsSet} object
\item[\code{snthresh}] signal to noise ratio cutoff
\item[\code{scales}] scales of CWT
\item[\code{nearbyPeak}] Determine whether to include the nearby small peaks of
major peaks. TRUE by default
\item[\code{sleep}] number of seconds to pause between plotting peak finding cycles

\item[\code{verbose.columns}] additional peak meta data columns are returned 

\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This is a wrapper around the peak picker in the bioconductor package
MassSpecWavelet calling 'cwt', 'get.localMaximum.cwt',
'get.ridge', 'identify.majorPeaks' and tuneIn.peakInfo.
\end{Details}
\begin{Value}
A matrix with columns:

\begin{ldescription}
\item[\code{mz}] m/z value of the peak at the centroid position

\item[\code{mzmin}] m/z value at the start-point of the peak

\item[\code{mzmax}] m/z value at the end-point of the peak

\item[\code{rt}] always -1

\item[\code{rtmin}] always -1

\item[\code{rtmax}] always -1

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

\item[\code{maxo}] intensity of original (raw) peak at the centroid position

\item[\code{intf}] always NA 

\item[\code{maxf}] maximum MSW-filter response of the peak

\item[\code{sn}] Signal/Noise ratio
\end{ldescription}
\end{Value}
\begin{Section}{Methods}
\describe{
\item[object = "xcmsRaw"] \code{
    findPeaks.MSW(object, snthresh=3,
    scales=seq(1,22,3), nearbyPeak=TRUE,
    peakScaleRange=5, amp.Th=0.01,
    minNoiseLevel=amp.Th/SNR.Th,
    ridgeLength=24, tuneIn=FALSE,
    sleep=0, verbose.columns = FALSE)
    }

}
\end{Section}
\begin{Author}\relax
Steffen Neumann, Joachim kutzera, \email{sneumann\textbar{}jkutzer@ipb-halle.de}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{findPeaks-methods}{findPeaks.Rdash.methods}}
\code{\LinkA{xcmsRaw-class}{xcmsRaw.Rdash.class}}
\code{\LinkA{peakDetectionCWT}{peakDetectionCWT}}
\end{SeeAlso}

