\HeaderA{aGFF-class}{Class for storing GFF-like data}{aGFF.Rdash.class}
\aliasA{plot,aGFF-method}{aGFF-class}{plot,aGFF.Rdash.method}
\aliasA{print,aGFF-method}{aGFF-class}{print,aGFF.Rdash.method}
\aliasA{show,aGFF-method}{aGFF-class}{show,aGFF.Rdash.method}
\keyword{classes}{aGFF-class}
\begin{Description}\relax
The GFF format is quite versatile while remaining simple.
This class simply stores the annotation associated with a set of GFF
files from the same regions of the genome along with some information
about the samples from which the data came and the data (from the
"score" column of the GFF file) themselves.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the
form \code{new("aGFF", ...).  Also, the \bsl{}code\{read.resultsGFF()\}
    function returns aGFF objects.}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{annotation}:] Object of class \code{"data.frame"} with
two columns absolutely necessary, "Chromosome" and "Location".
Other columns can be included.
\item[\code{data}:] Object of class \code{"matrix"} of the same
number of rows as the annotation slot and the same number of
columns as the number of rows in the samples slot, containing
data for later analysis
\item[\code{samples}:] Object of class \code{"data.frame"} for
describing the samples, one row per sample
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[plot] \code{signature(x = "aGFF")}: to plot a region along the
genome.
\item[print] \code{signature(x = "aGFF")}: simple method to display
summary of aGFF object
\item[show] \code{signature(object = "aGFF")}: simple method to display
summary of aGFF object
}
\end{Section}
\begin{Author}\relax
Sean Davis
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{read.resultsGFF}{read.resultsGFF}} and\code{\LinkA{aGFFCalc-class}{aGFFCalc.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# Load an example
data(example.agff)
example.agff
\end{ExampleCode}
\end{Examples}

