\HeaderA{xcmsRaw}{Constructor for xcmsRaw objects which reads NetCDF/mzXML files}{xcmsRaw}
\keyword{file}{xcmsRaw}
\begin{Description}\relax
This function handles the task of reading a NetCDF/mzXML file containing
LC/MS or GC/MS data into a new \code{xcmsRaw} object. It also
transforms the data into profile (maxrix) mode for efficient
plotting and data exploration.
\end{Description}
\begin{Usage}
\begin{verbatim}
xcmsRaw(filename, profstep = 1, profmethod = "intlin", profparam = list())
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{filename}] path name of the NetCDF or mzXML file to read
\item[\code{profstep}] step size (in m/z) to use for profile generation
\item[\code{profmethod}] method to use for profile generation
\item[\code{profparam}] extra parameters to use for profile generation
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
If \code{profstep} is set to 0, no profile matrix is generated.
Only first level MS data is read, not MS/MS, etc.)
\end{Details}
\begin{Value}
A \code{xcmsRaw} object.
\end{Value}
\begin{Note}\relax
\end{Note}
\begin{Author}\relax
Colin A. Smith, \email{csmith@scripps.edu}
\end{Author}
\begin{References}\relax
NetCDF file format:
\url{http://my.unidata.ucar.edu/content/software/netcdf/}

mzXML file format:
\url{http://sashimi.sourceforge.net/software_glossolalia.html}
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{xcmsRaw-class}{xcmsRaw.Rdash.class}},
\code{\LinkA{profStep}{profStep}},
\code{\LinkA{profMethod}{profMethod}}
\end{SeeAlso}

