\HeaderA{score\_fun}{Scoring for MS/MS spectra}{score.Rul.fun}
\begin{Description}\relax
A similarity scoring function for MS/MS spectra against a reference.
\end{Description}
\begin{Usage}
\begin{verbatim}
score_fun(ref, exp, method="distMatrix", ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{ref}] An array of numbers for the refference
\item[\code{exp}] An array of numbers for the test
\item[\code{method}] A string of either 'distMatrix' or 'cor'
\item[\code{...}] Any other arguments to be passed to other functions
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This is a starting method to score MS/MS data. Which reports the parameters to the various one of the scoreing functions.
\end{Details}
\begin{Value}
\begin{ldescription}
\item[\code{score}] Percentage score between the two arrays
\end{ldescription}
\end{Value}
\begin{Author}\relax
H. Paul Benton, \email{hpbenton@scripps.edu}
\end{Author}
\begin{References}\relax
H. Paul Benton, D.M. Wong, S.A.Strauger, G. Siuzdak "XC\eqn{MS^2}{}:"
Analytical Chemistry 2008 DOI:\url{http://pubs.acs.org/doi/abs/10.1021/ac800795f/}
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{score\_fun.distMatrix}{score.Rul.fun.distMatrix}},
\code{\LinkA{score\_fun.cor}{score.Rul.fun.cor}}
\end{SeeAlso}

