\name{Subset}
\alias{Subset}
\alias{Subset,flowFrame,filter-method}
\alias{Subset,flowSet,ANY-method}
\alias{Subset,flowFrame-method}
\alias{Subset,flowFrame,logical-method}
\alias{Subset,flowSet,list-method}
\alias{Subset,flowSet,filterResultList-method}
\alias{Subset,flowSet,ANY}

\title{Subset a flowFrame or a flowSet}

\description{ An equivalent of a \code{\link{subset}} function for
\code{\linkS4class{flowFrame}} or a \code{\linkS4class{flowSet}}
object. Alternatively, the regular subsetting operators can be used for
most of the topics documented here.
}

\usage{
Subset(x, subset, ...)
}

\arguments{
  
  \item{x}{The flow object, frame or set, to subset.}
  
  \item{subset}{A filter object or, in the case of \code{flowSet}
    subsetting, a named list of filters.}
  
  \item{\dots}{Like the original \code{\link{subset}} function, you can
    also select columns.}
  
}

\details{

The \code{Subset} method is the recommended method for obtaining a
\code{\linkS4class{flowFrame}} that only contains events consistent with
a particular filter. It is functionally equivalent to
\code{frame[as(filter(frame,subset),"logical"),]} when used in the
\code{\linkS4class{flowFrame}} context. Used in the
\code{\linkS4class{flowSet}} context, it is equivalent to using
\code{\link{fsApply}} to apply the filtering operation to each
\code{\linkS4class{flowFrame}}.

Additionally, using \code{Subset} on a \code{\linkS4class{flowSet}} can
also take a named \code{list} as the subset. In this case, the names of
the list object should correspond to the \code{sampleNames} of the
flowSet, allowing a different filter to be applied to each frame. If not
all of the names are used or excess names are present, a warning will be
generated but the valid filters will be applied for the rare instances
where this is the intended operation. Note that a \code{\link{filter}}
operation will generate a list of \code{\linkS4class{filterResult}}
objects that can be used directly with \code{Subset} in this manner.

}

\value{

Depending on the original context, either a
\code{\linkS4class{flowFrame}} or a \code{\linkS4class{flowSet}}.

}

\author{B. Ellis}

\seealso{\code{\link{split}}, \code{\link{subset}}}

\examples{

sample <- read.flowSet(path=system.file("extdata", package="flowCore"),
pattern="0877408774")
result <- filter(sample, rectangleGate("FSC-H"=c(-Inf, 1024)))
result
Subset(sample,result)

}

\keyword{manip}