\HeaderA{PreFilter-class}{Class PreFilter}{PreFilter.Rdash.class}
\aliasA{callFilter,PreFilter-method}{PreFilter-class}{callFilter,PreFilter.Rdash.method}
\aliasA{callFilter<-,PreFilter,character-method}{PreFilter-class}{callFilter<.Rdash.,PreFilter,character.Rdash.method}
\aliasA{cvFilter,PreFilter-method}{PreFilter-class}{cvFilter,PreFilter.Rdash.method}
\aliasA{cvFilter<-,PreFilter,numeric-method}{PreFilter-class}{cvFilter<.Rdash.,PreFilter,numeric.Rdash.method}
\aliasA{diffFilter,PreFilter-method}{PreFilter-class}{diffFilter,PreFilter.Rdash.method}
\aliasA{diffFilter<-,PreFilter,numeric-method}{PreFilter-class}{diffFilter<.Rdash.,PreFilter,numeric.Rdash.method}
\aliasA{gapFilter,PreFilter-method}{PreFilter-class}{gapFilter,PreFilter.Rdash.method}
\aliasA{gapFilter<-,PreFilter,numeric-method}{PreFilter-class}{gapFilter<.Rdash.,PreFilter,numeric.Rdash.method}
\aliasA{highFilter,PreFilter-method}{PreFilter-class}{highFilter,PreFilter.Rdash.method}
\aliasA{highFilter<-,PreFilter,character-method}{PreFilter-class}{highFilter<.Rdash.,PreFilter,character.Rdash.method}
\aliasA{lowFilter,PreFilter-method}{PreFilter-class}{lowFilter,PreFilter.Rdash.method}
\aliasA{lowFilter<-,PreFilter,character-method}{PreFilter-class}{lowFilter<.Rdash.,PreFilter,character.Rdash.method}
\aliasA{madFilter,PreFilter-method}{PreFilter-class}{madFilter,PreFilter.Rdash.method}
\aliasA{madFilter<-,PreFilter,numeric-method}{PreFilter-class}{madFilter<.Rdash.,PreFilter,numeric.Rdash.method}
\aliasA{quantileFilter,PreFilter-method}{PreFilter-class}{quantileFilter,PreFilter.Rdash.method}
\aliasA{quantileFilter<-,PreFilter,numeric-method}{PreFilter-class}{quantileFilter<.Rdash.,PreFilter,numeric.Rdash.method}
\aliasA{ratioFilter,PreFilter-method}{PreFilter-class}{ratioFilter,PreFilter.Rdash.method}
\aliasA{ratioFilter<-,PreFilter,numeric-method}{PreFilter-class}{ratioFilter<.Rdash.,PreFilter,numeric.Rdash.method}
\aliasA{varFilter,PreFilter-method}{PreFilter-class}{varFilter,PreFilter.Rdash.method}
\aliasA{varFilter<-,PreFilter,numeric-method}{PreFilter-class}{varFilter<.Rdash.,PreFilter,numeric.Rdash.method}
\keyword{classes}{PreFilter-class}
\begin{Description}\relax
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{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("PreFilter", ...)}. \\
Alternatively, the contructor \code{\LinkA{PreFilter}{PreFilter}} can be used.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{mad}:] Object of class \code{"list"} describing parameters for \code{madFilter}.
\item[\code{cv}:] Object of class \code{"list"} describing parameters for \code{cvFilter}.
\item[\code{variance}:] Object of class \code{"list"} describing parameters for \code{varFilter}.
\item[\code{difference}:] Object of class \code{"list"} describing parameters for \code{diffFilter}.
\item[\code{ratio}:] Object of class \code{"list"} describing parameters for \code{ratioFilter}.
\item[\code{gap}:] Object of class \code{"list"} describing parameters for \code{gapFilter}.
\item[\code{hithreshold}:] Object of class \code{"list"} describing parameters for \code{highFilter}.
\item[\code{lothreshold}:] Object of class \code{"list"} describing parameters for \code{lowFilter}.
\item[\code{quantile}:] Object of class \code{"list"} describing parameters for \code{quantileFilter}.
\item[\code{prescall}:] Object of class \code{"list"} describing parameters for \code{callFilter}.
\item[\code{numfilters}:] Object of class \code{"numeric"} giving the number of filters applied.
}
\end{Section}
\begin{Section}{Extends}
Class \code{"\LinkA{Filter}{Filter.Rdash.class}"}, directly.
\end{Section}
\begin{Section}{Methods}
\describe{
\item[callFilter] \code{signature(object = "PreFilter")}: extracts slot \code{prescall}.
\item[callFilter<-] \code{signature(object = "PreFilter", value = "character")}: replaces 
slot \code{prescall} with character vector c(cutoff, samples, condition).
\item[cvFilter] \code{signature(object = "PreFilter")}: extracts slot \code{cv}.
\item[cvFilter<-] \code{signature(object = "PreFilter", value = "numeric")}: replaces 
slot \code{cv} with numeric vector c(cutoff, trim, epsilon).
\item[diffFilter] \code{signature(object = "PreFilter")}: extracts slot \code{difference}.
\item[diffFilter<-] \code{signature(object = "PreFilter", value = "numeric")}: replaces 
slot \code{difference} with numeric vector c(cutoff, trim, epsilon).
\item[gapFilter] \code{signature(object = "PreFilter")}: extracts slot \code{gap}.
\item[gapFilter<-] \code{signature(object = "PreFilter", value = "numeric")}: replaces 
slot \code{gap} with numeric vector c(cutoff, window, trim, epsilon).
\item[highFilter] \code{signature(object = "PreFilter")}: extracts slot \code{hithreshold}.
\item[highFilter<-] \code{signature(object = "PreFilter", value = "character")}: replaces 
slot \code{hithreshold} with character vector c(cutoff, parameter, condition).
\item[lowFilter] \code{signature(object = "PreFilter")}: extracts slot \code{lothreshold}.
\item[lowFilter<-] \code{signature(object = "PreFilter", value = "character")}: replaces 
slot \code{lothreshold} with character vector c(cutoff, parameter, condition).
\item[madFilter] \code{signature(object = "PreFilter")}: extracts slot \code{mad}.
\item[madFilter<-] \code{signature(object = "PreFilter", value = "numeric")}: replaces 
slot \code{mad} with numeric vector c(cutoff, epsilon).
\item[quantileFilter] \code{signature(object = "PreFilter")}: extracts slot \code{quantile}.
\item[quantileFilter<-] \code{signature(object = "PreFilter", value = "numeric")}: replaces 
slot \code{quantile} with numeric vector c(cutoff, loquantile, hiquantile).
\item[ratioFilter] \code{signature(object = "PreFilter")}: extracts slot \code{ratio}.
\item[ratioFilter<-] \code{signature(object = "PreFilter", value = "numeric")}: replaces 
slot \code{ratio} with numeric vector c(cutoff).
\item[varFilter] \code{signature(object = "PreFilter")}: extracts slot \code{variance}.
\item[varFilter<-] \code{signature(object = "PreFilter", value = "numeric")}: replaces 
slot \code{variance} with numeric vector c(cutoff, trim, epsilon).
}
\end{Section}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{SeeAlso}\relax
related classes \code{\LinkA{Filter}{Filter.Rdash.class}}, \code{\LinkA{UniFilter}{UniFilter.Rdash.class}}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## for demonstration purposes only:  initialize all pre-filters
prefltr <- new("PreFilter")
madFilter(prefltr) <- c(0.5,0.01)
cvFilter(prefltr) <- c(0.3,0.0,0.01)
varFilter(prefltr) <- c(0.6,0.02,0.01)
diffFilter(prefltr) <- c(2.2,0.0,0.01)
ratioFilter(prefltr) <- c(1.5)
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")
quantileFilter(prefltr) <- c(3.0, 0.05, 0.95)
callFilter(prefltr) <- c(0.02,80.0,"percent")
str(prefltr)
\end{ExampleCode}
\end{Examples}

