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\title{SNP-level Classes used in the \Rpackage{oligoClasses} Package}
\author{Robert B. Scharpf}
\date{\today}

\begin{document}
\maketitle

\section{Introduction}

<<echo=FALSE>>=
library(oligoClasses)
@ 

This document provides an overview of the classes used to contain
SNP-level summaries from high-throughput SNP platforms, such as
Affymetrix.  These classes are used by the \R{} packages
\Rpackage{oligo}, \Rpackage{SNPchip}, and \Rpackage{VanillaICE}.  See
the \Rpackage{oligo} package for more details regarding the
feature-level classes.

<<diagram, echo=FALSE, eval=FALSE>>=
 source("dataClasses.R")
@ 

\begin{figure}[h]
  \includegraphics{SnpLevelClasses-diagram}
  \caption{Hierarchy of SNP-level classes.  Virtual classes are shaded.}
\end{figure}

SNP-level classes include 

\begin{itemize}
  
\item \Robject{SnpCallSet}: a class for genotype calls and confidence
  scores.  AssayData elements include \Robject{calls} and
  \Robject{callsConfidence}.
  
\item \Robject{SnpCopyNumberSet}: class for copy number and confidence
  scores.  AssayData elements include \Robject{copyNumber} and
  \Robject{cnConfidence}.
  
\item \Robject{oligoSnpSet}: class containing both genotype calls and
  copy number estimates, as well as the corresponding confidence
  scores.  AssayData elements include include the union of elements in
  \Robject{SnpCallSet} and \Robject{SnpCopyNumberSet}.
\end{itemize}

\end{document}