\HeaderA{"FCSmetadata-class"}{Class "FCSmetadata" Metadata portion of a Flow Cytometry Standard
object}{"FCSmetadata.Rdash.class"}
\aliasA{"FCSmetadata"}{"FCSmetadata-class"}{"FCSmetadata"}
\aliasA{"print-methods",FCSmetadata-method}{"FCSmetadata-class"}{"print.Rdash.methods",FCSmetadata.Rdash.method}
\aliasA{"show-methods",FCSmetadata-method}{"FCSmetadata-class"}{"show.Rdash.methods",FCSmetadata.Rdash.method}
\aliasA{"summary-methods",FCSmetadata-method}{"FCSmetadata-class"}{"summary.Rdash.methods",FCSmetadata.Rdash.method}
\aliasA{"[",FCSmetadata-method}{"FCSmetadata-class"}{"[",FCSmetadata.Rdash.method}
\aliasA{"[-methods",FCSmetadata-method}{"FCSmetadata-class"}{"[.Rdash.methods",FCSmetadata.Rdash.method}
\aliasA{"[<-",FCSmetadata-method}{"FCSmetadata-class"}{"[<.Rdash.",FCSmetadata.Rdash.method}
\aliasA{"[<--methods",FCSmetadata-method}{"FCSmetadata-class"}{"[<.Rdash..Rdash.methods",FCSmetadata.Rdash.method}
\aliasA{"[[",FCSmetadata-method}{"FCSmetadata-class"}{"[[",FCSmetadata.Rdash.method}
\aliasA{"[[-methods",FCSmetadata-method}{"FCSmetadata-class"}{"[[.Rdash.methods",FCSmetadata.Rdash.method}
\aliasA{"[[<-"-methods,FCSmetadata-method}{"FCSmetadata-class"}{"[[<.Rdash.".Rdash.methods,FCSmetadata.Rdash.method}
\aliasA{"[[<--methods",FCSmetadata-method}{"FCSmetadata-class"}{"[[<.Rdash..Rdash.methods",FCSmetadata.Rdash.method}
\aliasA{FCSmetadata}{"FCSmetadata-class"}{FCSmetadata}
\aliasA{FCSmetadata-class}{"FCSmetadata-class"}{FCSmetadata.Rdash.class}
\aliasA{print,FCSmetadata-method}{"FCSmetadata-class"}{print,FCSmetadata.Rdash.method}
\aliasA{print-methods,FCSmetadata-method}{"FCSmetadata-class"}{print.Rdash.methods,FCSmetadata.Rdash.method}
\aliasA{show,FCSmetadata-method}{"FCSmetadata-class"}{show,FCSmetadata.Rdash.method}
\aliasA{show-methods,FCSmetadata-method}{"FCSmetadata-class"}{show.Rdash.methods,FCSmetadata.Rdash.method}
\aliasA{summary,FCSmetadata-method}{"FCSmetadata-class"}{summary,FCSmetadata.Rdash.method}
\aliasA{summary-methods,FCSmetadata-method}{"FCSmetadata-class"}{summary.Rdash.methods,FCSmetadata.Rdash.method}
\aliasA{[,FCSmetadata-method}{"FCSmetadata-class"}{[,FCSmetadata.Rdash.method}
\aliasA{[-methods,FCSmetadata-method}{"FCSmetadata-class"}{[.Rdash.methods,FCSmetadata.Rdash.method}
\aliasA{[<-,FCSmetadata-method}{"FCSmetadata-class"}{[<.Rdash.,FCSmetadata.Rdash.method}
\aliasA{[<--methods,FCSmetadata-method}{"FCSmetadata-class"}{[<.Rdash..Rdash.methods,FCSmetadata.Rdash.method}
\aliasA{[[,FCSmetadata-method}{"FCSmetadata-class"}{[[,FCSmetadata.Rdash.method}
\aliasA{[[-methods,FCSmetadata-method}{"FCSmetadata-class"}{[[.Rdash.methods,FCSmetadata.Rdash.method}
\aliasA{[[<-,FCSmetadata-method}{"FCSmetadata-class"}{[[<.Rdash.,FCSmetadata.Rdash.method}
\aliasA{[[<--methods,FCSmetadata-method}{"FCSmetadata-class"}{[[<.Rdash..Rdash.methods,FCSmetadata.Rdash.method}
\keyword{classes}{"FCSmetadata-class"}
\begin{Description}\relax
Information from the HEADER and TEXT of a raw binary FCS
file about the data and other parameters are stored in the metadata.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("FCSmetadata", ...)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{mode}:] Object of class \code{"character"} the "\$MODE" mode of
the raw binary FCS file
\item[\code{size}:] Object of class \code{"numeric"} the "\$TOT" row
dimension of the data; describing the number of observations or
cells 
\item[\code{nparam}:] Object of class \code{"numeric"} the "\$PAR" column
dimension of the data; describing the number of parameters 
\item[\code{shortnames}:] Object of class \code{"vector"} the "\$PnN"
short names corresponding to the column variables of the data; these
names are generally non-descript and are not used as the names of the
columns of the data
\item[\code{longnames}:] Object of class \code{"vector"} the "\$PnS"
long names used for the column variables of the data
\item[\code{paramranges}:] Object of class \code{"vector"} the
"\$PnR" maximum value corresponding to the column variables
\item[\code{filename}:] Object of class \code{"character"} path and/or
name of the \bold{original} raw binary FCS object  
\item[\code{objectname}:] Object of class \code{"character"} the
name of the original, \code{FCS-class} object
\item[\code{original}:] Object of class \code{"logical"} the
original status of the current object 
\item[\code{fcsinfo}:] Object of class \code{"list"} the other
parameters and values in the HEADER and TEXT of the raw binary FCS
file 
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item["["] \code{signature(x = "FCSmetadata")}: Extracts the metadata
slots or metadata@fcsinfo slots by using a single character name
index; Extracts the metadata@fcsinfo slots by using a single or
vector of numerical indicies  

\item["[<-"] \code{signature(x = "FCSmetadata")}: Replaces the metadata
slots or metadata@fcsinfo slots by using a single character name
index; Replaces the metadata@fcsinfo slots by using a single or
vector of numerical indicies;Adds a new slot to the
metadata@fcsinfo 

\item["[["] \code{signature(x = "FCSmetadata")}:  Extracts the metadata
slots or metadata@fcsinfo slots by using a single character name
index; Extracts the metadata@fcsinfo slots by using a single or
vector of numerical indicies 

\item["[[<-"] \code{signature(x = "FCSmetadata")}: Replaces the metadata
slots or metadata@fcsinfo slots by using a single character name
index; Replaces the metadata@fcsinfo slots by using a single or
vector of numerical indicies;Adds a new slot to the
metadata@fcsinfo

\item["print-methods"] \code{signature(x = "FCSmetadata")}: prints the
original status, the objectname, filename, and dimensions of the
data

\item["show-methods"] \code{signature(object = "FCSmetadata")}: same as 'print' 

\item["summary-methods"] \code{signature(object = "FCSmetadata")}: summaries
the metadata in a string output 
}
\end{Section}
\begin{Note}\relax
For more information about the different parameters in the
metadata@fcsinfo slot, please look at the documentation for
\code{read.FCS}.
\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{read.FCS}{read.FCS}}, 
\code{\LinkA{"FCS-class"}{"FCS.Rdash.class"}},
\code{\LinkA{"print-methods"}{"print.Rdash.methods"}},
\code{\LinkA{"show-methods"}{"show.Rdash.methods"}},
\code{\LinkA{"summary-methods"}{"summary.Rdash.methods"}},
\code{\LinkA{"[-methods"}{"[.Rdash.methods"}},
\code{\LinkA{"[[-methods"}{"[[.Rdash.methods"}},
\code{\LinkA{"[<--methods"}{"[<.Rdash..Rdash.methods"}},
\code{\LinkA{"[[<--methods"}{"[[<.Rdash..Rdash.methods"}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
default<-new("FCSmetadata")

some.meta<-new("FCSmetadata", fcsinfo=list("comment"=rep("none", 10)),
mode="none", nparam=0, size=0)

## extract/subset the metadata
some.meta[["nparam"]]
some.meta["paramranges"]
## replace the metadata/subsetassign the metadata
## 3 parameters with ranges
some.meta[["nparam"]]<-3
some.meta["paramranges"]<-rep(1,3)
## show
show(some.meta)
## print
print(some.meta)
some.meta
## summary
summary(some.meta)
\end{ExampleCode}
\end{Examples}

