\HeaderA{aGFFCalc-class}{Class "aGFFCalc"}{aGFFCalc.Rdash.class}
\aliasA{plot,aGFFCalc-method}{aGFFCalc-class}{plot,aGFFCalc.Rdash.method}
\aliasA{print,aGFFCalc-method}{aGFFCalc-class}{print,aGFFCalc.Rdash.method}
\aliasA{show,aGFFCalc-method}{aGFFCalc-class}{show,aGFFCalc.Rdash.method}
\keyword{classes}{aGFFCalc-class}
\begin{Description}\relax
Store results of ACME calculations
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("aGFFCalc", ...)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{call}:] Object of class \code{"call"}, contains the
exact call to do.aGFF.calc, for historical purposes
\item[\code{threshold}:] Object of class \code{"numeric"}, the
threshold used in the calculation
\item[\code{cutpoints}:] Object of class \code{"numeric"}, the data
value above which probes were considered positive
\item[\code{vals}:] Object of class \code{"matrix"}, equivalent in
size to the original data matrix, containing the calculated
p-values from the ACME algorithm
\item[\code{annotation}:] Object of class \code{"data.frame"},
currently a copy of the original annotation, possibly reordered in
chromosome order 
\item[\code{data}:] Object of class \code{"matrix"}, the original
data, possibly reordered
\item[\code{samples}:] Object of class \code{"data.frame"}, sample
metadata
}
\end{Section}
\begin{Section}{Extends}
Class \code{"aGFF"}, directly.
\end{Section}
\begin{Section}{Methods}
\describe{
\item[plot] \code{signature(x = "aGFFCalc", ask=FALSE)}: plot the results of an
ACME calculation
\item[print] \code{signature(x = "aGFFCalc")}: brief overview of the
object
\item[show] \code{signature(object = "aGFFCalc")}: brief overview of
the object
}
\end{Section}
\begin{Author}\relax
Sean Davis <sdavis2@mail.nih.gov>
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{do.aGFF.calc}{do.aGFF.calc}}, \code{\LinkA{aGFF-class}{aGFF.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(example.agff)
example.agffcalc <- do.aGFF.calc(example.agff,window=1000,thresh=0.9)
example.agffcalc
\end{ExampleCode}
\end{Examples}

