\HeaderA{SMAPObservations}{Constructor for "SMAPObservations" objects}{SMAPObservations}
\keyword{classes}{SMAPObservations}
\begin{Description}\relax
A constructor for
\code{\LinkA{SMAPObservations-class}{SMAPObservations.Rdash.class}} objects.
\end{Description}
\begin{Usage}
\begin{verbatim}
SMAPObservations(value, chromosome, startPosition, endPosition,
                 name=character(0),
                 reporterId=as.character(1:length(value)))
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{value}] A vector of microarray intensity ratios (numeric).
\item[\code{chromosome}] A vector of chromosome annotations (character).
\item[\code{startPosition}] A vector of start positions (numeric).
\item[\code{endPosition}] A vector of end positions (numeric).
\item[\code{name}] The name of the observation set (character).
\item[\code{reporterId}] A vector of observation identifiers, e.g., probe ids
(character).
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The vectors \code{value}, \code{chromosome}, \code{startPosition},
\code{endPosition}, and \code{reporterId} must be of equal length.
\end{Details}
\begin{Value}
An object of class
\code{\LinkA{SMAPObservations-class}{SMAPObservations.Rdash.class}}.
\end{Value}
\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-class}{SMAPObservations.Rdash.class}},
\code{\LinkA{SMAPHMM-class}{SMAPHMM.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Load Glioblastoma multiforme data
data(GBM)
observations <- SMAPObservations(value=as.numeric(GBM[,2]),
                                 chromosome=as.character(GBM[,3]),
                                 startPosition=as.numeric(GBM[,4]),
                                 endPosition=as.numeric(GBM[,5]),
                                 name="G24460",
                                 reporterId=as.character(GBM[,1]))
## plot observations
plot(observations, ylim=c(0,2))
## plot subset of observations (chromosome 9)
ids <- which(chromosome(observations) == "9")
plot(observations[ids])
\end{ExampleCode}
\end{Examples}

