\HeaderA{findIsotopes-methods}{Deconvolute/Annotate LC/ESI-MS data}{findIsotopes.Rdash.methods}
\aliasA{findIsotopes}{findIsotopes-methods}{findIsotopes}
\aliasA{findIsotopes,xsAnnotate-method}{findIsotopes-methods}{findIsotopes,xsAnnotate.Rdash.method}
\keyword{methods}{findIsotopes-methods}
\begin{Description}\relax
Annotate isotope peaks for a xsAnnotate object. Returns a xsAnnotate object with annotated isotopes.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] the \code{xsAnnotate} object
\item[\code{maxcharge}] max. number of the isotope charge
\item[\code{maxiso}] max. number of the isotope peaks
\item[\code{ppm}] ppm error for the search
\item[\code{mzabs}] allowed variance for the search
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Isotope peaks are annotated for a xsAnnotate object according to given rules (maxcharge, maxiso). The algorithm benefits from a earlier grouping of the data, with groupFWHM and groupCorr. Generates a list of all possible isotopes, which is stored in object@isotopes.
\end{Details}
\begin{Section}{Methods}
\describe{
\item[object = "xsAnnotate"] \code{findIsotopes(object,maxcharge=3,maxiso=3,ppm=5,mzabs=0.01)}

}
\end{Section}
\begin{Author}\relax
Carsten Kuhl \textless{}ckuhl@ipb-halle.de\textgreater{}
\end{Author}
\begin{Examples}
\begin{ExampleCode}
 library(CAMERA)
 file <- system.file('mzdata/MM14.mzdata', package = "CAMERA")
 xs   <- xcmsSet(file, method="centWave", ppm=30, peakwidth=c(5,10))
 an   <- xsAnnotate(xs)
 an   <- groupFWHM(an)
 an   <- findIsotopes(an)
\end{ExampleCode}
\end{Examples}

