\HeaderA{SMAPObservations-class}{Class "SMAPObservations": A class to manage microarray
observations for the SMAP package}{SMAPObservations.Rdash.class}
\aliasA{chromosome}{SMAPObservations-class}{chromosome}
\aliasA{endPosition}{SMAPObservations-class}{endPosition}
\aliasA{name}{SMAPObservations-class}{name}
\aliasA{noObservations}{SMAPObservations-class}{noObservations}
\aliasA{plot,SMAPObservations,missing-method}{SMAPObservations-class}{plot,SMAPObservations,missing.Rdash.method}
\aliasA{reporterId}{SMAPObservations-class}{reporterId}
\aliasA{startPosition}{SMAPObservations-class}{startPosition}
\aliasA{value}{SMAPObservations-class}{value}
\keyword{classes}{SMAPObservations-class}
\begin{Description}\relax
Holds observed microarray intensity ratios and clone
annotations for the \pkg{SMAP} package.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form
\code{new("SMAPObservations", value, chromosome, startPosition,
        endPosition, name, reporterId)}.  You can also use the convenience
function \code{\LinkA{SMAPObservations}{SMAPObservations}}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{value}:] Object of class \code{"numeric"} Microarray
intensity ratios.
\item[\code{chromosome}:] Object of class \code{"character"}
Associated chromosomes for the observations.
\item[\code{startPosition}:] Object of class \code{"numeric"}
Associated start positions for the observations.
\item[\code{endPosition}:] Object of class \code{"numeric"}
Associated end positions for the observations.
\item[\code{reporterId}:] Object of class \code{"character"}
Identifiers of the observations, e.g., probe ids.
\item[\code{name}:] Object of class \code{"character"} An identifier
of the observation set.
\item[\code{noObservations}:] Object of class \code{"numeric"} The
number of observations in the set.
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[value] \code{signature(object = "SMAPObservations")}: Returns
the values of the observations.
\item[chromosome] \code{signature(object = "SMAPObservations")}:
Returns the chromosome annotations of the observations.
\item[startPosition] \code{signature(object = "SMAPObservations")}:
Returns the start positions of the observations.
\item[endPosition] \code{signature(object = "SMAPObservations")}:
Returns the end positions of the observations.
\item[reporterId] \code{signature(object = "SMAPObservations")}:
Returns the identifiers of the observations.
\item[name] \code{signature(object = "SMAPObservations")}: Returns
the name of the observation set.
\item[noObservations] \code{signature(object = "SMAPObservations")}:
Returns the number of observations in the set.
\item[initialize] \code{signature(.Object = "SMAPObservations")}:
Creates an instance.
\item[plot] \code{signature(x = "SMAPObservations", y = "missing")}:
A plot method for the observations.
\item[[] \code{signature(x = "SMAPPObservations")}: Creates a new
object of class SMAPObservations with extracted elements as
specified by the indices provided.
}
\end{Section}
\begin{Author}\relax
Robin Andersson, \email{robin.andersson@lcb.uu.se}
\end{Author}
\begin{References}\relax
Andersson, R., Bruder, C. E. G., Piotrowski, A., Menzel, U., Nord, H.,
Sandgren, J., Hvidsten, T. R., Diaz de Stahl, T., Dumanski, J. P.,
Komorowski, J., A Segmental Maximum A Posteriori Approach to Array-CGH
Copy Number Profiling, submitted
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{smap}{smap}},
\code{\LinkA{SMAPObservations}{SMAPObservations}}
\end{SeeAlso}

