\name{flowFP-class}
\docType{class}
\alias{flowFP-class}

\title{Fingerprint class description.}

\description{
This class represents fingerprints generated from a model derived
from a \link[flowCore:flowFrame-class]{flowFrame} or 
\link[flowCore:flowSet-class]{flowSet}.
}

\section{Objects from the Class}{
Objects are created by calling the constructor \link{flowFP}.
}

\section{Slots}{
	 \describe{
    \item{\code{counts}:}{This matrix is organized such that rows correspond 
                          to individual \emph{flowFrame}s, and columns to 
                          the bins in the underlying \code{flowFPModel}.  A
                          matrix element thus represents the number of events in
                          a single bin from a single \emph{flowFrame}.
                          The sum of each row will equal the total number of events in
                          the corresponding \emph{flowFrame}.
     }
    \item{\code{tags}:}{This list specifies the bin number to which each event is assigned.
                        There is a list element for each instance in the object.  Each
                        list element is a integer vector whose length is the number of
                        events in the corresponding \emph{flowFrame}.
     }
    \item{\code{sampleNames}:}{Names of instances, taken from the flowSet on
                               construction.}
    \item{\code{sampleClasses}:}{Factor object describing the category of each 
                                 instance. (e.g. "Normal" or "Diseased")}
	\item{\code{name}:}{Inherited from \link{flowFPModel}.}
    \item{\code{parameters}:}{Inherited from \link{flowFPModel}.}
    \item{\code{nRecursions}:}{Inherited from \link{flowFPModel}.}
    \item{\code{trainingSet}:}{Inherited from \link{flowFPModel}.}
    \item{\code{trainingSetParams}:}{Inherited from \link{flowFPModel}.}
    \item{\code{dequantize}:}{Inherited from \link{flowFPModel}.}
    \item{\code{split_val}:}{Inherited from \link{flowFPModel}.}
    \item{\code{split_axis}:}{Inherited from \link{flowFPModel}.}
    \item{\code{binBoundary}:}{Inherited from \link{flowFPModel}.}
    \item{\code{.cRecursions}:}{Inherited from \link{flowFPModel}.}
    \item{\code{.tmp_tags}:}{Inherited from \link{flowFPModel}.}
  }
}
\section{Extends}{
Class \linkS4class{flowFPModel}, directly.
}
\section{Methods}{
  \describe{
    \item{[}{\code{signature(x = "flowFP", i = "ANY")}: ... }
    \item{counts}{\code{signature(object = "flowFP")}: ... }
    \item{length}{\code{signature(x = "flowFP")}: ... }
    \item{nbins}{\code{signature(object = "flowFP")}: ... }
    \item{sampleClasses}{\code{signature(object = "flowFP")}: ... }
    \item{tags}{\code{signature(object = "flowFP")}: ... }
    \item{show}{Shows the contents of the fingerprint object.}
    \item{summary}{Gives a summary of the fingerprint object.}
	 }
}
\references{
M. Roederer, et. al. (2001) Probability Binning Comparison: A Metric for Quantitating 
Multivariate Distribution Differences, \emph{Cytometry} \bold{45}, 47-55.

W. Rogers et. al. (2008) Cytometric Fingerprinting: Quantitative Characterization of 
Multivariate Distributions, \emph{Cytometry Part A} \bold{73}, 430-441.
}
\author{
Herb Holyst <\email{holyst@mail.med.upenn.edu}>, Wade Rogers <\email{rogersw@mail.med.upenn.edu}>
}

\seealso{ 
	\link{flowFP}, \link{flowFPModel}
}

\examples{

	# load a flowSet to use as an example.
	library(flowFP)
	data(fs1)
	model <- flowFPModel(fs1, parameters=c(4,5), nRecursions=6)
	
	fp <- flowFP(fs1, model)
	
	plot(fp)
	
}
\keyword{classes}