\HeaderA{PreFilter-constructor}{Constructor for Class PreFilter}{PreFilter.Rdash.constructor}
\aliasA{PreFilter}{PreFilter-constructor}{PreFilter}
\keyword{manip}{PreFilter-constructor}
\begin{Description}\relax
Constructor for class  PreFilter allows to apply different filters to class
\code{\LinkA{ExprTreeSet}{ExprTreeSet}}, i.e. to the expression level data.frame \code{data}.
\end{Description}
\begin{Usage}
\begin{verbatim}
PreFilter(mad         = character(),
          cv          = character(),
          variance    = character(),
          difference  = character(),
          ratio       = character(),
          gap         = character(),
          lothreshold = character(),
          hithreshold = character(),
          quantile    = character(),
          prescall    = character())
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{mad}] \code{"character"} vector describing parameters for \code{\LinkA{madFilter}{madFilter}}.
\item[\code{cv}] \code{"character"} vector describing parameters for \code{\LinkA{cvFilter}{cvFilter}}.
\item[\code{variance}] \code{"character"} vector describing parameters for \code{\LinkA{varFilter}{varFilter}}.
\item[\code{difference}] \code{"character"} vector describing parameters for \code{\LinkA{diffFilter}{diffFilter}}.
\item[\code{ratio}] \code{"character"} vector describing parameters for \code{\LinkA{ratioFilter}{ratioFilter}}.
\item[\code{gap}] \code{"character"} vector describing parameters for \code{\LinkA{gapFilter}{gapFilter}}.
\item[\code{lothreshold}] \code{"character"} vector describing parameters for \code{\LinkA{lowFilter}{lowFilter}}.
\item[\code{hithreshold}] \code{"character"} vector describing parameters for \code{\LinkA{highFilter}{highFilter}}.
\item[\code{quantile}] \code{"character"} vector describing parameters for \code{\LinkA{quantileFilter}{quantileFilter}}.
\item[\code{prescall}] \code{"character"} vector describing parameters for \code{\LinkA{callFilter}{callFilter}}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The PreFilter constructor allows to apply the following filters to class \code{\LinkA{ExprTreeSet}{ExprTreeSet}}:
\Tabular{lll}{
& \code{mad}:& character vector c(cutoff,epsilon). \\
& \code{cv}:& character vector c(cutoff,trim,epsilon). \\
& \code{variance}:& character vector c(cutoff,trim,epsilon). \\
& \code{difference}:& character vector c(cutoff,trim,epsilon). \\
& \code{ratio}:& character vector c(cutoff). \\
& \code{gap}:& character vector c(cutoff,window,trim,epsilon). \\
& \code{lothreshold}:& character vector c(cutoff,parameter,condition). \\
& \code{hithreshold}:& character vector c(cutoff,parameter,condition). \\
& \code{quantile}:& character vector c(cutoff,loquantile,hiquantile). \\
& \code{prescall}:& character vector c(cutoff,samples,condition). 
}
\end{Details}
\begin{Value}
An object of type \code{"\LinkA{PreFilter}{PreFilter.Rdash.class}"}
\end{Value}
\begin{Note}\relax
Function \code{PreFilter} is used as constructor for class \code{PreFilter} so that the user
need not know details for creating S4 classes.
\end{Note}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{Filter}{Filter.Rdash.class}}, \code{\LinkA{UniFilter}{UniFilter}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## fill character vectors within constructor
prefltr <- PreFilter(mad=c(0.5,0.01), prescall=c(0.002, 6,"samples"),
                     lothreshold=c(6.0,0.02,"mean"), hithreshold=c(10.5,80.0,"percent"))
str(prefltr)

## alternatively add character vectors as methods after creation of constructor
prefltr <- PreFilter()
madFilter(prefltr) <- c(0.5,0.01)
gapFilter(prefltr) <- c(0.3,0.05,0.0,0.01)
lowFilter(prefltr) <- c(4.0,3,"samples")
highFilter(prefltr) <- c(14.5,75.0,"percent")
str(prefltr)
\end{ExampleCode}
\end{Examples}

