\HeaderA{AnnotatedSnpSet-class}{Class "AnnotatedSnpSet"}{AnnotatedSnpSet.Rdash.class}
\aliasA{alleleA,AnnotatedSnpSet-method}{AnnotatedSnpSet-class}{alleleA,AnnotatedSnpSet.Rdash.method}
\aliasA{alleleB,AnnotatedSnpSet-method}{AnnotatedSnpSet-class}{alleleB,AnnotatedSnpSet.Rdash.method}
\aliasA{chromosome,AnnotatedSnpSet-method}{AnnotatedSnpSet-class}{chromosome,AnnotatedSnpSet.Rdash.method}
\aliasA{chromosomeAnnotation,AnnotatedSnpSet-method}{AnnotatedSnpSet-class}{chromosomeAnnotation,AnnotatedSnpSet.Rdash.method}
\aliasA{chromosomeAnnotation<-,AnnotatedSnpSet,data.frame-method}{AnnotatedSnpSet-class}{chromosomeAnnotation<.Rdash.,AnnotatedSnpSet,data.frame.Rdash.method}
\aliasA{coerce,AnnotatedSnpSet,AnnotatedSnpCopyNumberSet-method}{AnnotatedSnpSet-class}{coerce,AnnotatedSnpSet,AnnotatedSnpCopyNumberSet.Rdash.method}
\aliasA{dbSnpId,AnnotatedSnpSet-method}{AnnotatedSnpSet-class}{dbSnpId,AnnotatedSnpSet.Rdash.method}
\aliasA{enzyme,AnnotatedSnpSet-method}{AnnotatedSnpSet-class}{enzyme,AnnotatedSnpSet.Rdash.method}
\aliasA{fData,AnnotatedSnpSet-method}{AnnotatedSnpSet-class}{fData,AnnotatedSnpSet.Rdash.method}
\aliasA{fragmentLength,AnnotatedSnpSet-method}{AnnotatedSnpSet-class}{fragmentLength,AnnotatedSnpSet.Rdash.method}
\aliasA{plotCytoband,AnnotatedSnpSet-method}{AnnotatedSnpSet-class}{plotCytoband,AnnotatedSnpSet.Rdash.method}
\aliasA{plotSnp,AnnotatedSnpSet-method}{AnnotatedSnpSet-class}{plotSnp,AnnotatedSnpSet.Rdash.method}
\aliasA{position,AnnotatedSnpSet-method}{AnnotatedSnpSet-class}{position,AnnotatedSnpSet.Rdash.method}
\aliasA{smoothSnp,AnnotatedSnpSet-method}{AnnotatedSnpSet-class}{smoothSnp,AnnotatedSnpSet.Rdash.method}
\keyword{classes}{AnnotatedSnpSet-class}
\begin{Description}\relax
Container for genotype and copy number data from SNP chips,
as well as chromosome-level features
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("AnnotatedSnpSet", phenoData, assayData, experimentData, featureData, annotation, chromosomeAnnotation)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{chromosomeAnnotation}:] Object of class
\code{data.frame} containing chromosome-level annotation 
\item[\code{assayData}:] Object of class \code{AssayData}
containing copy number and genotype call matrices 
\item[\code{phenoData}:] Object of class \code{AnnotatedDataFrame}  
\item[\code{featureData}:] Object of class
\code{AnnotatedDataFrame}.  Contains annotation for the SNP's,
such as chromosome, physical position, and alleles. 
\item[\code{experimentData}:] Object of class \code{MIAME}  
\item[\code{annotation}:] Character string for type of SNP
chip. e.g., "pd.mapping50k.xba240"
\item[\code{.\_\_classVersion\_\_}:] Object of class \code{Versions}  
}
\end{Section}
\begin{Section}{Extends}
Class \code{AnnotatedSnpCallSet}, directly.
Class \code{AnnotatedSnpCopyNumberSet}, directly.
Class \code{SnpCallSet}, by class AnnotatedSnpCallSet, distance 2.
Class \code{eSet}, by class AnnotatedSnpCallSet, distance 3.
Class \code{VersionedBiobase}, by class AnnotatedSnpCallSet, distance 4.
Class \code{Versioned}, by class AnnotatedSnpCallSet, distance 5.
Class \code{SnpCopyNumberSet}, by class AnnotatedSnpCopyNumberSet, distance 2.
Class \code{eSet}, by class AnnotatedSnpCopyNumberSet, distance 3.
Class \code{VersionedBiobase}, by class AnnotatedSnpCopyNumberSet, distance 4.
Class \code{Versioned}, by class AnnotatedSnpCopyNumberSet, distance 5.
\end{Section}
\begin{Section}{Methods}
\describe{
\item[alleleA] \code{signature(object="AnnotatedSnpSet")}: return
the A allele for the specified SNPs in object

\item[alleleB] \code{signature(object="AnnotatedSnpSet")}: return
the B allele for the specified SNPs in object

\item[chromosome] \code{signature(object="AnnotatedSnpSet")}:
accessor for the chromosome

\item[fData] \code{signature(object="AnnotatedSnpSet")}:
accessor for the data.frame containing feature-level annotation.
Usually very large.    

\item[fragmentLength] \code{signature(object="AnnotatedSnpSet")}:
accessor for the length of the PCR fragment on which the SNP resides    

\item[plotCytoband] \code{signature(object="AnnotatedSnpSet")}:
Plots the cytoband for a single chromosome.

\item[plotSnp] \code{signature(object="AnnotatedSnpSet", ...)}: Makes a
scatterplot of copy number (vertical axis) versus physical
position (horizontal axis) for each chromosome and sample in the
AnnotatedSnpSet object.  Points are color-coded by the genotype
call.

\item[position] \code{signature(object="AnnotatedSnpSet")}: Returns
physical position of SNP along the chromosome in numbers of
basepairs from the 5' end (an integer)
}
\end{Section}
\begin{Note}\relax
\end{Note}
\begin{Author}\relax
Rob Scharpf
\end{Author}
\begin{References}\relax
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{plotSnp}{plotSnp}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(annSnpset)
annSnpset
##for formatting the plot layout, see the vignette
plotSnp(annSnpset, 1:10, 1:2)
\end{ExampleCode}
\end{Examples}

