\HeaderA{xcmsSet}{Constructor for xcmsSet objects which finds peaks in NetCDF/mzXML files}{xcmsSet}
\keyword{file}{xcmsSet}
\begin{Description}\relax
This function handles the construction of xcmsSet objects. It
finds peaks in batch mode and pre-sorts files from subdirectories
into different classes suitable for grouping.
\end{Description}
\begin{Usage}
\begin{verbatim}
xcmsSet(files = NULL, snames = NULL, sclass = NULL,
        profmethod = "bin", profparam = list(), ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{files}] path names of the NetCDF/mzXML files to read
\item[\code{snames}] sample names
\item[\code{sclass}] sample classes
\item[\code{profmethod}] method to use for profile generation
\item[\code{profparam}] parameters to use for profile generation
\item[\code{...}] further arguments to the \code{findPeaks} method of the
\code{xcmsRaw} class

\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The default values of the \code{files}, \code{snames}, and
\code{sclass} arguments cause the function to recursively search
for readable files. The filename without extention is used for the
sample name. The subdirectory path is used for the sample class.
\end{Details}
\begin{Value}
A \code{xcmsSet} object.
\end{Value}
\begin{Note}\relax
\end{Note}
\begin{Author}\relax
Colin A. Smith, \email{csmith@scripps.edu}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{xcmsSet-class}{xcmsSet.Rdash.class}},
\code{\LinkA{findPeaks}{findPeaks}},
\code{\LinkA{profStep}{profStep}},
\code{\LinkA{profMethod}{profMethod}}
\end{SeeAlso}

