\name{filter-and-methods}
\docType{methods}
\alias{intersectFilter-method}
\alias{subsetFilter-method}
\alias{\%&\%}
\alias{\%&\%-methods}
\alias{\%&\%,ANY-method}
\alias{\%&\%,filter,filter-method}
\alias{\%subset\%,ANY-method}
\alias{\%subset\%}
\alias{&,filter,filter-method}
\alias{&,filter,list-method}
\alias{&,list,filter-method}
\alias{\%subset\%,filter,filter-method}
\alias{\%subset\%,list,filter-method}
\alias{coerce,intersectFilter,call-method}

\title{Take the intersection of two filters}

\description{

  There are two notions of intersection in \code{flowCore}. First, there
  is the usual intersection boolean operator \code{&} that has been
  overridden to allow the intersection of two filters or of a filter and
  a list for convenience. There is also the \code{\%&\%} or
  \code{\%subset\%} operator that takes an intersection, but with subset
  semantics rather than simple intersection semantics. In other words,
  when taking a subset, calculations from
  \code{\link[flowCore]{summary}} and other methods are taken with
  respect to the right hand filter. This primarily affects percentage
  calculations, which are ordinarily calculated with respect to the
  entire population as well as data-driven gating procedures which will
  operate only on elements contained by the right hand filter.  This
  becomes especially important when using filters such as
  \code{\link[flowCore]{norm2Filter}}

}

\author{B. Ellis}
\keyword{methods}