\HeaderA{fmatch-methods}{Index of matching peaks}{fmatch.Rdash.methods}
\aliasA{fmatch,Massvector,Massvector-method}{fmatch-methods}{fmatch,Massvector,Massvector.Rdash.method}
\aliasA{fmatch,numeric,numeric-method}{fmatch-methods}{fmatch,numeric,numeric.Rdash.method}
\keyword{methods}{fmatch-methods}
\keyword{manip}{fmatch-methods}
\begin{Description}\relax
Determines index of matching peaks.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{obx}] see below in \bold{Methods} section
\item[\code{oby}] see below in \bold{Methods} section
\item[\code{error}] measurement error in \emph{e.g.} Da or as relative error
in parts per million (ppm)
\item[\code{ppm}] if \code{TRUE} then error in parts per million(ppm), in
arbitrary units otherwise.
\item[\code{uniq}] if \code{TRUE} compute non-crossing matching.
\end{ldescription}
\end{Arguments}
\begin{Value}
\begin{ldescription}
\item[\code{plind}] index of matching peaks in argument \code{obx}
\item[\code{calind}] index of matching peaks in argument \code{oby}
\item[\code{resid}] residue between matching peaks (either in \code{ppm} or \code{Da}) 
\end{ldescription}
\end{Value}
\begin{Section}{Methods}
\describe{
\item[obx = "numeric", oby = "numeric"] ...
\item[obx = "Massvector", oby = "Massvector"] ...
}
\end{Section}
\begin{Examples}
\begin{ExampleCode}
data(pldata)
pl1 <- pldata[[1]]
pl2 <- pldata[[4]]
fmatch(pl1,pl2,error=0.1,ppm=FALSE,uniq=TRUE)
fmatch(pl1,pl2,error=150,ppm=TRUE,uniq=TRUE)
\end{ExampleCode}
\end{Examples}

