\HeaderA{extractGateHistory}{Extracting the gating information from the history}{extractGateHistory}
\keyword{data}{extractGateHistory}
\keyword{manip}{extractGateHistory}
\begin{Description}\relax
The history string corresponding to a specific gating Index specified
by 'gateNum' is retrieved and output as a list of specific components.
\end{Description}
\begin{Usage}
\begin{verbatim}
extractGateHistory(x, gateNum)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] a "FCSgate" object created after using \code{\LinkA{createGate}{createGate}}
\item[\code{gateNum}] the numeric column position of the gating index in
the 'gate' matrix 
\end{ldescription}
\end{Arguments}
\begin{Value}
\begin{ldescription}
\item[\code{gateNum}] the numeric column position of the gating index in
the 'gate' matrix
\item[\code{gateName}] character name of the gating index specified in the
'gate' matrix
\item[\code{type}] type of gating (ie, "biscut", "uniscut", "bipcut",
"bidcut")
\item[\code{biscut.quadrant}] the quadrant specified (ie, ("+/+", "-/-",
"+/-", "-/+"))
\item[\code{data.colpos}] the gated parameter column positions in the
'data' matrix
\item[\code{data.colnames}] the gated parameter column names in the 'data'
matrix
\item[\code{IndexValue.In}] the value of the index that specifies inclusion
or selection
\item[\code{gatingrange}] the vector of gating threshold(s)
\item[\code{prev.gateNum}] the previous or most prior gating index column
position in the 'gate' matrix
\item[\code{prev.gateName}] the previous or most prior gating index column
name in the 'gate' matrix
\item[\code{comment}] character string of the user-defined comment
\end{ldescription}
\end{Value}
\begin{Author}\relax
A.J. Rossini and J.Y. Wan
\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{FCS-class}{FCS.Rdash.class}}, \code{\LinkA{FCSgate-class}{FCSgate.Rdash.class}},
\code{\LinkA{createGate}{createGate}, \\code\{\LinkA{createGate}{createGate}\}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
 if (require(rfcdmin)) {
      data.there<-is.element("MC.053",objects())
      if ((sum(data.there) != length(data.there))) {
        ## obtaining the FCS objects from VRC data
        data(MC.053min)
      }
  
####  foo1 : Gating type: uniscut, univariate single cut
foo1 <- createGate(MC.053, varpos=4, gatingrange=256,
                    type="uniscut", MY.DEBUG=TRUE)

#### foo2.3 : Gating type : biscut -/-
foo2.3 <- createGate(foo1, varpos=c(1,2),
                      gatingrange=c(256, 300),
                      type="biscut",
                      biscut.quadrant="-/-",
                      prev.gateNum=NULL,
                      MY.DEBUG=TRUE)

## obtain gate information for first uniscut gate
gate.info1<-extractGateHistory(foo1, gateNum=1)

## obtain gate information for the second biscut gate
gate.info2<-extractGateHistory(foo2.3, gateNum=2)

### foo2.3.1 : extraction
foo2.3.1 <- extractGatedData(foo2.3, gateNum=2,
                              IndexValue.In=1,
                              MY.DEBUG=TRUE)
## obtain the second biscut gate information after
## subset/extraction of row observations
gate.info2.1<-extractGateHistory(foo2.3.1, gateNum=2)
}
\end{ExampleCode}
\end{Examples}

