\HeaderA{cwt}{Continuous Wavelet Transform (CWT)}{cwt}
\keyword{methods}{cwt}
\begin{Description}\relax
CWT(Continuous Wavelet Transform) with Mexican Hat wavelet (by default) to match the peaks in Mass Spectrometry spectrum
\end{Description}
\begin{Usage}
\begin{verbatim}
cwt(ms, scales = 1, wavelet = "mexh")
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{ms}] Mass Spectrometry spectrum (a vector of MS intensities)
\item[\code{scales}] a vector represents the scales at which to perform CWT. 
\item[\code{wavelet}] The wavelet base, Mexican Hat by default. User can provide wavelet Psi(x) as a form of two row matrix. The first 
row is the x value, and the second row is Psi(x) corresponding to x.  
\end{ldescription}
\end{Arguments}
\begin{Value}
The return is the 2-D CWT coefficient matrix, with column names as the scale. Each column is the CWT coefficients at that scale.
\end{Value}
\begin{Author}\relax
Pan Du, Simon Lin
\end{Author}
\begin{Examples}
\begin{ExampleCode}
        data(exampleMS)
        scales <- seq(1, 64, 3)
        wCoefs <- cwt(exampleMS[5000:11000], scales=scales, wavelet='mexh')

        ## Plot the 2-D CWT coefficients as image (It may take a while!)
        xTickInterval <- 1000
        image(5000:11000, scales, wCoefs, col=terrain.colors(256), axes=FALSE, xlab='m/z index', ylab='CWT coefficient scale', main='CWT coefficients')
        axis(1, at=seq(5000, 11000, by=xTickInterval))
        axis(2, at=c(1, seq(10, 64, by=10)))
        box()
\end{ExampleCode}
\end{Examples}

