\HeaderA{highFilter-methods}{Upper Threshold Filter}{highFilter.Rdash.methods}
\aliasA{highFilter}{highFilter-methods}{highFilter}
\aliasA{highFilter<\Rdash}{highFilter-methods}{highFilter<.Rdash.}
\keyword{methods}{highFilter-methods}
\begin{Description}\relax
This method initializes the Upper Threshold Filter. \\
The \code{cutoff} value defines the upper threshold for allowed expression levels. If e.g.
the number of samples exceeding this cutoff value is greater than \code{parameter} then the
corresponding dataframe row is flagged, i.e. \code{flag = 0}. \\
The Upper Threshold Filter flags all rows with: \code{flag = (sum(expression[i] <= cutoff) >= parameter)}

\emph{Usage}

\code{highFilter(object)} \\
\code{highFilter(object, value)<-}
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] object of class \code{PreFilter}.
\item[\code{value}] character vector \code{c(cutoff, parameter, condition)}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The method \code{highFilter} initializes the following parameters:
\Tabular{lll}{
& \code{cutoff}:& the upper threshold level for the filter. \\
& \code{parameter}:& this value depends on the \code{condition} used: \\
& \code{condition}:& \code{condition="samples"}:    number of samples (default): \\
&                  & \code{condition="percent"}:    percent of samples. \\
&                  & \code{condition="mean"}:       mean value of samples. \\
&                  & \code{condition="percentile"}: percentile of samples.
}
\end{Details}
\begin{Value}
An initialized \code{\LinkA{PreFilter}{PreFilter.Rdash.class}} object.
\end{Value}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{Examples}
\begin{ExampleCode}
prefltr <- PreFilter()
highFilter(prefltr) <- c(14.5,75.0,"percent")
str(prefltr)
\end{ExampleCode}
\end{Examples}

