\HeaderA{score\_fun.cor}{Scoring for MS/MS spectra Via correlation}{score.Rul.fun.cor}
\begin{Description}\relax
A similarity scoring function for MS/MS spectra against a reference via correlation.
\end{Description}
\begin{Usage}
\begin{verbatim}
  score_fun.cor(ref, exp)
\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
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
A score system using correlation analysis to correlate two arrays. If the arrays are a different length then the system will buffer the shorter one with 0s.
\end{Details}
\begin{Value}
\begin{ldescription}
\item[\code{score}] Correlation 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}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Not run: 
score<-xcms:::score_fun.cor(rnorm(10), rnorm(10))
score

a<-abs(rnorm(5))
a[2]<-xcms:::ppmDev(a[2], 30)
score<-xmcs:::score_fun.cor()
score
## End(Not run)
\end{ExampleCode}
\end{Examples}

