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\name{VAFilterResult-class}
\docType{class}
\alias{VAFilterResult-class}
\alias{VAFilterResult}
\alias{Logic,VAFilterResult,VAFilterResult-method}
\alias{!,VAFilterResult-method}
\alias{name,VAFilterResult-method}
\alias{show,VAFilterResult-method}
\alias{stats}
\alias{stats,VAFilterResult-method}
\title{"VAFilterResult" for VAFilter output and statistics}
\description{
Objects of this class are logical vectors indicating records passing
the applied filter, with an associated data frame summarizing the
name, input number of records, records passing filter, and logical
operation used for all filters in which the result participated.
}
\usage{
VAFilterResult(data = GRanges(), x = logical(), name = NA_character_,
subset = TRUE, input = length(x), passing = sum(x), op = NA_character_)
\S4method{Logic}{VAFilterResult,VAFilterResult}(e1, e2)
\S4method{name}{VAFilterResult}(x, ...)
stats(x, ...)
\S4method{show}{VAFilterResult}(object)
}
\arguments{
\item{data}{A \code{linkS4class{GRanges}} of the data to be filtered.
}
\item{x, object, e1, e2}{For \code{VAFilterResult}, \code{logical()}
indicating records that passed filter or, for others, an instance of
\code{VAFilterResult} class.
}
\item{name}{\code{character()} indicating the name by which the filter
is to be referred. Internally, \code{name}, \code{input},
\code{passing}, and \code{op} may all be vectors representing
columns of a \code{data.frame} summarizing the application of
successive filters.
}
\item{subset}{\code{logical()} when TRUE, the function returns a
subset of the data that passed the filter as a
\code{linkS4class{GRanges}} object. The \code{name} and \code{stats}
information are in the metadata slot. When FALSE, an object of
\code{VAFilterResult} is returned.
}
\item{input}{\code{integer()} indicating the length of the original
input.
}
\item{passing}{\code{integer()} indicating the number of records
passing the filter.
}
\item{op}{\code{character()} indicating the logical operation, if any,
associated with this filter.
}
\item{\dots}{Additional arguments, unused in methods documented on this
page.
}
}
\section{Objects from the Class}{
Objects can be created through \code{\link{VAFilterResult}}, but these
are automatically created by the application of \code{\link{vaFilter}}
instances.
}
\section{Slots}{
\describe{
\item{\code{.Data}:}{Object of class \code{"logical"} indicating
records that passed the filter. }
\item{\code{name}:}{Object of class \code{"ScalarCharacter"}
representing the name of the filter whose results are
summarized. The name is either the actual name of the filter, or a
combination of filter names and logical operations when the
outcome results from application of several filters in a single
logical expression. }
\item{\code{stats}:}{Object of class \code{"data.frame"} summarizing
the name, input number of records, records passing filter, and
logical operation used for all filters in which the result
participated. The \code{data.frame} rows correspond either to
single filters, or to logical combinations of filters.}
}
}
\section{Methods}{
\describe{
\item{Logic}{\code{signature(e1 = "VAFilterResult", e2 =
"VAFilterResult")}: logic operations on filters.}
\item{!}{\code{signature(x = "VAFilterResult")}: Negate the outcome
of the current filter results }
\item{name}{\code{signature(x = "VAFilterResult")}: The name of the
filter that the results are based on.}
\item{stats}{\code{signature(x = "VAFilterResult")}: a
\code{data.frame} as described in the \sQuote{Slots} section of
this page.}
\item{show}{\code{signature(object = "VAFilterResult")}: summary of
filter results.}
}
}
\author{Valerie Obenchain <vobencha@fhcrc.org>}
\seealso{\code{\link{VAFilter}}}
\examples{
## see ?VAFilter
}
\keyword{classes}
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