\HeaderA{fcs.type}{Objects providing parameters for the raw FCS file types}{fcs.type}
\aliasA{FCS.type}{fcs.type}{FCS.type}
\aliasA{fcs.type.cellquest.3.1.FACS.Vantage}{fcs.type}{fcs.type.cellquest.3.1.FACS.Vantage}
\aliasA{fcs.type.cellquest.3.1.FACScan}{fcs.type}{fcs.type.cellquest.3.1.FACScan}
\aliasA{fcs.type.cellquest.3.3}{fcs.type}{fcs.type.cellquest.3.3}
\aliasA{fcs.type.default}{fcs.type}{fcs.type.default}
\aliasA{fcs.type.DiVa1024}{fcs.type}{fcs.type.DiVa1024}
\aliasA{fcs.type.FACSCalibur1024}{fcs.type}{fcs.type.FACSCalibur1024}
\aliasA{fcs.type.facscan1024}{fcs.type}{fcs.type.facscan1024}
\aliasA{fcs.type.facscan256}{fcs.type}{fcs.type.facscan256}
\aliasA{fcs.type.FACStar256}{fcs.type}{fcs.type.FACStar256}
\aliasA{fcs.type.LSR1024}{fcs.type}{fcs.type.LSR1024}
\aliasA{fcs.type.LSR256}{fcs.type}{fcs.type.LSR256}
\aliasA{fcs.type.LYSYS}{fcs.type}{fcs.type.LYSYS}
\keyword{environment}{fcs.type}
\begin{Description}\relax
The \code{fcs.type} objects define the parameters needed for reading
in certain raw FCS files into R via the use of \code{\LinkA{read.FCS}{read.FCS}}.
Currently this is just a script file defining certain \code{fcs.type}
objects, but ultimately this will be an environment.  There are
certain \code{\LinkA{read.FCS}{read.FCS}} parameters that are known to be
compatible for certain types of cytometers.  The \code{fcs.type}
objects may be optionally used during the reading in of raw FCS files
into R and result in FCS R-objects (FCS objects).
\end{Description}
\begin{Usage}
\begin{verbatim}
   fcs.type.default
\end{verbatim}
\end{Usage}
\begin{Arguments}
No arguments.
\end{Arguments}
\begin{Details}\relax
A fcs.type is a list of the following:
\item[version] raw FCS version number; value$=$"1.0" or "2.0" or "3.0"
\item[byte.size] The byte size for the file (8 bits is one byte);
value=1 or 2 or 4, etc.
\item[signed] boolean; If the data is signed; value$=$FALSE or TRUE
\item[endian] The endian of the file depending on the endian of the
platform; Usually the value of endian is "big" (if both the file and
platform endian are "big") or "little" (if both the platform and the
file endian are "little") or  "auto", then the read.FCS will
automatically detect the endian compatibility with the platform
system (See \code{\LinkA{readBin}{readBin}} for more details.) 

The fcs.types are the following:
\item[1.  fcs.type.default] a list of the following options and values: 
\item[version] "2.0"
\item[byte.size] 2
\item[signed] TRUE
\item[endian] "auto"

\item[2.  fcs.type.cellquest.3.1.FACScan] a list of the following options
and values:
\item[version] "2.0"
\item[byte.size] 1
\item[signed] FALSE
\item[endian] "auto"

\item[3.  fcs.type.LSR256] a list of the following options
and values:
\item[version] "2.0"
\item[byte.size] 1
\item[signed] FALSE
\item[endian] "auto"

\item[4.  fcs.type.FACStar256] a list of the following options
and values:
\item[version] "2.0"
\item[byte.size] 1
\item[signed] FALSE
\item[endian] "auto"

\item[5.  fcs.type.facscan256] a list of the following options
and values:
\item[version] "2.0"
\item[byte.size] 1
\item[signed] FALSE
\item[endian] "auto"

\item[6.  fcs.type.cellquest.3.1.FACS.Vantage] a list of the following options and values: 
\item[version] "2.0"
\item[byte.size] 2
\item[signed] TRUE
\item[endian] "auto"

\item[7.  fcs.type.cellquest.3.3] a list of the following options and values: 
\item[version] "2.0"
\item[byte.size] 2
\item[signed] TRUE
\item[endian] "auto"

\item[8.  fcs.type.LYSYS] a list of the following options and values: 
\item[version] "2.0"
\item[byte.size] 2
\item[signed] TRUE
\item[endian] "auto"

\item[9.  fcs.type.DiVa1024] a list of the following options and values: 
\item[version] "2.0"
\item[byte.size] 2
\item[signed] TRUE
\item[endian] "auto"

\item[10. fcs.type.FACSCalibur1024] a list of the following options and values: 
\item[version] "2.0"
\item[byte.size] 2
\item[signed] TRUE
\item[endian] "auto"

\item[11. fcs.type.LSR1024] a list of the following options and values: 
\item[version] "2.0"
\item[byte.size] 2
\item[signed] TRUE
\item[endian] "auto"

\item[12. fcs.type.facscan1024] a list of the following options and values: 
\item[version] "2.0"
\item[byte.size] 2
\item[signed] TRUE
\item[endian] "auto"
\end{Details}
\begin{Value}
With the help of fcs.type, the raw FCS file will be read into a
FCS R object that can be implemented for further analysis in R.
\end{Value}
\begin{Author}\relax
A.J. Rossini and J.Y. Wan
\end{Author}
\begin{References}\relax
Peter Rabinovitch
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{read.FCS}{read.FCS}},
\code{\LinkA{readBin}{readBin}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

  if (require(rfcdmin)) {
    ## obtaining the location of the fcs files in the data
    get.path<-function(filename) {
      datadir<-system.file("fcs", package="rfcdmin")
      return(paste(datadir, filename, sep="/"))
    }


    FF256 <-read.FCS(get.path("facscan256.fcs"),
                              fcs.type=fcs.type.facscan256)
  }

\end{ExampleCode}
\end{Examples}

