\HeaderA{findPeaks.matchedFilter-methods}{Feature detection in the chromatographic time domain}{findPeaks.matchedFilter.Rdash.methods}
\aliasA{findPeaks.matchedFilter}{findPeaks.matchedFilter-methods}{findPeaks.matchedFilter}
\aliasA{findPeaks.matchedFilter,xcmsRaw-method}{findPeaks.matchedFilter-methods}{findPeaks.matchedFilter,xcmsRaw.Rdash.method}
\keyword{methods}{findPeaks.matchedFilter-methods}
\begin{Description}\relax
Find peaks in extracted the chromatographic time domain of the profile
matrix.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] \code{xcmsRaw} object
\item[\code{fwhm}] full width at half maximum of matched filtration gaussian model
peak

\item[\code{sigma}] standard deviation of matched filtration model peak

\item[\code{max}] maximum number of peaks per extracted ion chromatogram

\item[\code{snthresh}] signal to noise ratio cutoff
\item[\code{step}] step size to use for profile generation
\item[\code{steps}] number of steps to merge prior to filtration
\item[\code{mzdiff}] minimum difference in m/z for peaks with overlapping retention
times

\item[\code{index}] return indicies instead of values for m/z and retention times

\item[\code{sleep}] number of seconds to pause between plotting peak finding cycles

\end{ldescription}
\end{Arguments}
\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{intf}] integrated area of filtered peak

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

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

\item[\code{i}] rank of peak identified in merged EIC (\textless{}= \code{max})

\item[\code{sn}] signal to noise ratio of the peak

\end{ldescription}
\end{Value}
\begin{Section}{Methods}
\describe{
\item[object = "xcmsRaw"] \code{
    findPeaks.matchedFilter(object, fwhm = 30, sigma = fwhm/2.3548, max = 5, 
    snthresh = 10, step = 0.1, steps = 2, mzdiff = 0.8 - step*steps, 
    index = FALSE, sleep = 0)
  }

}
\end{Section}
\begin{Author}\relax
Colin A. Smith, \email{csmith@scripps.edu}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{findPeaks-methods}{findPeaks.Rdash.methods}}
\code{\LinkA{xcmsRaw-class}{xcmsRaw.Rdash.class}}
\end{SeeAlso}

