\HeaderA{"FCSgate-class"}{Class "FCSgate" Flow Cytometry Standard extension to gating}{"FCSgate.Rdash.class"}
\aliasA{"FCSgate"}{"FCSgate-class"}{"FCSgate"}
\aliasA{FCSgate}{"FCSgate-class"}{FCSgate}
\aliasA{FCSgate-class}{"FCSgate-class"}{FCSgate.Rdash.class}
\keyword{classes}{"FCSgate-class"}
\begin{Description}\relax
This class of objects extends the class \code{FCS-class}
to incorporate information from gating which is a procedure by which
rows or cells from the data are selected via one or two dimensional
value restrictions or gating ranges.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("FCSgate", ...)}.
Essentially this new object includes the \code{FCS-class} object.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{gate}:] Object of class \code{"matrix"} containing the
gating indices such that each column corresponds to a different
gating procedure/index and the rows correspond to the positions of
the \bold{original} row/cell observations. 

\item[\code{history}:] Object of class \code{"vector"} containing the
gating history strings such that each vector element corresponds
to a different gating procedure/index and each string contains
information about the particular gate, column variables that were
used, and other additional comments.

\item[\code{extractGatedData.msg}:] Object of class \code{"vector"}
containing strings describing any extraction that took place
corresponding to each gating procedure/index and history string; each
string contains information about the particular corresponding
gate column position and gate name and what value index was for
inclusion/selection (ie, IndexValue.In)

\item[\code{current.data.obs}:] Object of class \code{"vector"}
contains the current data positional values from the original data 
\item[\code{data}:] Object of class \code{"matrix"} which holds
integer data such that the columns are the variables (usually
immunofluorescence measurements) and the rows are the cell
observations. 
\item[\code{metadata}:] Object of class \code{"FCSmetadata"} which
holds information about the file, data, and column variables among
other items in the header of the original raw FCS binary file. 
}
\end{Section}
\begin{Section}{Extends}
Class \code{"FCS"}, directly.
\end{Section}
\begin{Section}{Methods}
No methods defined with class "FCSgate" in the signature.
\end{Section}
\begin{Note}\relax
The methods \code{createGate} and \code{icreateGate}, functionally
without plots
or interactively with plots, respectively, extends the
\code{FCS-class} to the
FCSgate-class.  Some interactive gating schemes are noted in \code{FHCRC.HVTNFCS}
and \code{VRC.HVTNFCS}.  Further testing after gating is implemented by
\code{runflowcytests} on the particular variable of interest which is
usually the Interferon Gamma Immunofluoroescence measurement.
\end{Note}
\begin{Author}\relax
A.J. Rossini, J.Y. Wan, and Zoe Moodie
\end{Author}
\begin{References}\relax
Trevor Hastie, Robert Tibshirani, and Jerome Friedman. The
Elements of Statistical Learning: Data Mining, Inference, and
Prediction. Springer Series in Statistics : New York, 2001. pp.279-283.

Jerome H. Friedman and Nicholas I. Fisher. Bump Hunting in
High-Dimensional Data. Tech Report. October 28, 1998.

J. Paul Robinson, et al. Current Protocols in Cytometry.  John Wiley
\& Sons, Inc : 2001.

Mario Roederer and Richard R. Hardy. Frequency Difference Gating: A
Multivariate Method for Identifying Subsets that Differe between
Samples. Cytometry, 45:56-64, 2001.

Mario Roederer and Adam Treister and Wayne Moore and Leonore
A. Herzenberg. Probability Binning Comparison: A Metric for
Quantitating Univariate Distribution Differences. Cytometry, 45:37-46,
2001.

Keith A. Baggerly. Probability Binning and Testing Agreement between
Multivariate Immunofluorescence Histograms: Extending the Chi-Squared
Test. Cytometry, 45:141-150, 2001.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{createGate}{createGate}},
\code{\LinkA{icreateGate}{icreateGate}},
\code{\LinkA{extractGatedData}{extractGatedData}},
\code{\LinkA{extractGateHistory}{extractGateHistory}},
\code{\LinkA{FHCRC.HVTNFCS}{FHCRC.HVTNFCS}},
\code{\LinkA{VRC.HVTNFCS}{VRC.HVTNFCS}},
\code{\LinkA{"FCS-class"}{"FCS.Rdash.class"}},
\code{\LinkA{runflowcytests}{runflowcytests}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
default.FCSgateobj<-new("FCSgate")
\end{ExampleCode}
\end{Examples}

