\HeaderA{FHCRC.HVTNFCS}{Fred Hutchinson Cancer Research Center Sequential Gating
Procedure proposed by Julie McElrath's Lab}{FHCRC.HVTNFCS}
\keyword{iplot}{FHCRC.HVTNFCS}
\begin{Description}\relax
This function uses \code{\LinkA{icreateGate}{icreateGate}} and \code{\LinkA{createGate}{createGate}} to
select the datapoints which are of particular interest.  The selection
process is realized in an index column which is added to the data of
the FCS object.  In particular, after a series of gating/datapoint
selection sequences, the interferon gamma variable is of interest.

To row reduce the data of the FCS object, the function,
\code{\LinkA{extractGatedData}{extractGatedData}} should be used on the last gate index to
obtain the rows/cells and then should be used again to subset
across columns to obtain the gamma interferon column.
\end{Description}
\begin{Usage}
\begin{verbatim}

FHCRC.HVTNFCS(myFCSobj, gate1.vars = c(1, 2), gate2.vars = c(5, 7),
                 gate3.vars = c(3, 4),MY.DEBUG = FALSE)

\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{myFCSobj}] a FCS object
\item[\code{gate1.vars}] The vector of column variable positions
corresponding to Forward Scatter and Side Scatter variables for the
first gate; default
is column positions 1 and 2 respectively
\item[\code{gate2.vars}] The vector of column variable positions
corresponding to cd3 and cd8 variables for the
second gate; default is column positions 5 and 7 respectively
\item[\code{gate3.vars}] The vector of column variable positions
corresponding to cd69 and Interferon Gamma variables for gate 3;
default is column positions 3 and 4 respectively
\item[\code{MY.DEBUG}] if TRUE, then will print the debugging statements;
otherwise, if FALSE, then will surpress the debugging statements;
default is FALSE
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The Selection Sequence made by Julie McElrath's Lab is the following:

\item[\bold{gate1:bidcut:}] Forward Scatter VS Side Scatter
\item[single gate ] (Select the lymphocytes--central cluster) 

\item[\bold{gate2:bidcut:}] cd3 VS cd8
\item[gate 2.1:] (Select cd3+/cd8-)
\item[gate 2.2:] (Select cd3+/cd8+)


\item[\bold{gate3:biscut:}] cd69 vs Interferon Gamma
\item[gate 3.1:] (Select +/+ which are the cd4+ cells (from gate2.1))
\item[gate 3.2:] (Select +/+ which are the cd8+ cells (from gate2.2))


In General, the types of Gating/Cutting that are used in this gating
scheme are the following:

\item[uniscut = univariate single cut] (Selection of the positive/right half)

\item[biscut = bivariate single cut] (Selection of the +/-, -/-. +/+, or -/+ quadrant)

\item[bidcut = bivariate double cut] (Selection of the center rectangle
that results)
\end{Details}
\begin{Value}
\begin{ldescription}
\item[\code{FCS object}] with the following slots:
\item[\code{data}] A augmented dataframe with the added-on gating column variables/indices
\item[\code{metadata}] a FCSmetadata object with the information about the
gating column variables: \$PnR (gating range), \$PnN
(gating variable's shortname/unused name in the data of the FCS
object), \$PnS (gating variable's longname/used name), and other slot information
\end{ldescription}
\end{Value}
\begin{Section}{WARNING}
This gating scheme is not standard, and there may
have been changes to the gating scheme.  This gating scheme only
serves as an example, which demonstrates the use of
\code{\LinkA{createGate}{createGate}},\code{\LinkA{icreateGate}{icreateGate}}
and \code{\LinkA{"[[-methods"}{"[[.Rdash.methods"}} which extracts the metadata information
(eg. in order to obatin information about a previous gating
index/column variable
\end{Section}
\begin{Note}\relax
The "FHCRC" data from the \pkg{rfcdorig} package can be used for this sequential
gating scheme.
\end{Note}
\begin{Author}\relax
A.J. Rossini and J.Y. Wan
\end{Author}
\begin{References}\relax
Julie McElrath, PhD
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{createGate}{createGate}}, \code{\LinkA{icreateGate}{icreateGate}},
\code{\LinkA{showgate.FCS}{showgate.FCS}},
\code{\LinkA{VRC.HVTNFCS}{VRC.HVTNFCS}}, \code{\LinkA{plotvar.FCS}{plotvar.FCS}},
\code{\LinkA{"[-methods"}{"[.Rdash.methods"}}, \code{\LinkA{"[[-methods"}{"[[.Rdash.methods"}}
\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)
    }

    if (interactive()==TRUE){
      par(mfrow=c(4,2))

      MC.053.FHCRC<-FHCRC.HVTNFCS(MC.053)
    }
  }

\end{ExampleCode}
\end{Examples}

