\HeaderA{plotSnp}{Plots copy number and genotype calls against physical position}{plotSnp}
\aliasA{plot,ParSnpCallSet,SnpCallSet-method}{plotSnp}{plot,ParSnpCallSet,SnpCallSet.Rdash.method}
\aliasA{plot,ParSnpCopyNumberSet,SnpCopyNumberSet-method}{plotSnp}{plot,ParSnpCopyNumberSet,SnpCopyNumberSet.Rdash.method}
\aliasA{plot,ParSnpSet,oligoSnpSet-method}{plotSnp}{plot,ParSnpSet,oligoSnpSet.Rdash.method}
\aliasA{plot,SnpLevelSet-method}{plotSnp}{plot,SnpLevelSet.Rdash.method}
\aliasA{plotSnp,ParSnpCallSet,SnpCallSet-method}{plotSnp}{plotSnp,ParSnpCallSet,SnpCallSet.Rdash.method}
\aliasA{plotSnp,ParSnpCopyNumberSet,SnpCopyNumberSet-method}{plotSnp}{plotSnp,ParSnpCopyNumberSet,SnpCopyNumberSet.Rdash.method}
\aliasA{plotSnp,ParSnpSet,oligoSnpSet-method}{plotSnp}{plotSnp,ParSnpSet,oligoSnpSet.Rdash.method}
\aliasA{plotSnp,SnpLevelSet-method}{plotSnp}{plotSnp,SnpLevelSet.Rdash.method}
\keyword{hplot}{plotSnp}
\begin{Description}\relax
Returns an object inheriting from class \code{ParESet} -- essentially,
a list of default graphical parameters that can be modified as needed.
The \code{show} method for this class plots the copy number and
genotype calls versus physical position for an arbitrary number of
samples and chromosomes.
\end{Description}
\begin{Usage}
\begin{verbatim}
plotSnp(object, hmmPredict, ...)
## S4 method for signature 'SnpLevelSet':
plot(x, y, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object, x}] An object extending \code{ParESet}
\item[\code{hmmPredict, y}] An object of class \code{HmmPredict}
\item[\code{...}] Additional arguments to the initialization methods of
the \code{ParESet} classes
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
See examples in the vignette
\end{Details}
\begin{Author}\relax
R. Scharpf
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{par}{par}},
\code{\LinkA{ParESet-class}{ParESet.Rdash.class}},
\code{\LinkA{ParSnpCallSet-class}{ParSnpCallSet.Rdash.class}},
\code{\LinkA{ParSnpCopyNumberSet-class}{ParSnpCopyNumberSet.Rdash.class}},
\code{\LinkA{ParSnpSet-class}{ParSnpSet.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(sample.snpset)
chr1 <- sample.snpset[chromosome(sample.snpset) == "1", 1]
graph.par <- plotSnp(chr1)
class(graph.par)
## Not run: 
graph.par
## End(Not run)
\end{ExampleCode}
\end{Examples}

