\name{xcmsSet}
\alias{xcmsSet}
\title{Constructor for xcmsSet objects which finds peaks in NetCDF/mzXML files}
\description{
  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.
}
\usage{
xcmsSet(files = NULL, snames = NULL, sclass = NULL, phenoData = NULL,
        profmethod = "bin", profparam = list(),
        polarity = NULL, lockMassFreq=FALSE,
		mslevel=NULL, nSlaves=0, progressCallback=NULL,
                scanrange = NULL, ...)
}
\arguments{
  \item{files}{path names of the NetCDF/mzXML files to read}
  \item{snames}{sample names}
  \item{sclass}{sample classes}
    \item{phenoData}{sample names and classes}
  \item{profmethod}{method to use for profile generation}
  \item{profparam}{parameters to use for profile generation}
  \item{polarity}{filter raw data for positive/negative scans}
	\item{lockMassFreq}{Performs correction for Waters LockMass function}
    \item{mslevel}{perform peak picking on data of given mslevel}
    \item{nSlaves}{number of slaves/cores to be used for parallel peak detection.
		   MPI is used if installed, otherwise the snow package is employed for multicore support.}
  \item{progressCallback}{function to be called, when progressInfo changes (useful for GUIs)}
  \item{scanrange}{scan range to read}
  \item{\dots}{
    further arguments to the \code{findPeaks} method of the
    \code{xcmsRaw} class
  }
}
\details{
  The default values of the \code{files}, \code{snames}, \code{sclass}, and
  \code{phenoData} 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.
  If the files contain both positive and negative spectra, the polarity
  can be selected explicitly. The default (NULL) is to read all scans.

  The lock mass correction allows for the lock mass scan to be added back in
  with the last working scan. This correction gives better reproducibility 
  between sample sets.
}
\value{
  A \code{xcmsSet} object.
}
\author{Colin A. Smith, \email{csmith@scripps.edu}}
\note{
  
}
\seealso{
  \code{\link{xcmsSet-class}},
  \code{\link{findPeaks}},
  \code{\link{profStep}},
  \code{\link{profMethod}},
  \code{\link{xcmsPapply}}
}
\keyword{file}