%\VignetteDepends{GenomicFeatures}
%\VignetteIndexEntry{Annotation Packages}
%\VignettePackage{HTSandGeneCentricLabs}

\documentclass{beamer}

\usepackage{BioconductorSlides}
\SweaveOpts{keep.source=TRUE}

\title{Annotation Packages}
\author{Marc Carlson }
\institute[FHCRC]{Fred Hutchinson Cancer Research Center}
\date{July 28th 2010}

\begin{document}

<<setup, echo=FALSE>>=
options(width = 64)
@

\frame{\titlepage}

\begin{frame}[t]
  \frametitle{\Bioconductor{} Annotation Packages}
\begin{figure}[ht]
 \centering
  \includegraphics[width=4in,height=3in]{databaseTypes}
\end{figure}
\end{frame}



\begin{frame}[t]
  \frametitle{The newest addition are \Bioconductor{} Transcript DBs}
  \begin{block}{\Biocpkg{The GenomicFeatures package}}
    \begin{itemize}
      \item Transcript information stored in SQLite databases
      \item These databases attempt to represent the relational
        nature of splicing data correctly
      \item Transcript information exposed to user via the
        \Biocpkg{GenomicRanges} infrastructure
      \item Parsers are available to construct these databases from biomaRt
        or the UCSC genome browser.  Also there is a generic parser for
        custom jobs.
    \end{itemize}
  \end{block}
\end{frame}


\begin{frame}[t,fragile]
  \frametitle{Some transcript sources for \Biocpkg{GenomicFeatures}}
  \begin{block}{Constructors}
    \Rfunction{makeTranscriptDbFromBiomart},
    \Rfunction{makeTranscriptDbFromUCSC}
  \end{block}
{\footnotesize
<<loadGenomicFeatures>>=
library(GenomicFeatures)
nrow(supportedUCSCtables())
head(supportedUCSCtables(), 10)
@
}
\end{frame}


\begin{frame}{The \Rclass{TranscriptDb} schema}
  \begin{figure}
    \includegraphics[width=4.25in]{transcriptschema.png}
  \end{figure}
\end{frame}


\begin{frame}[t]
  \frametitle{Future \Bioconductor{} Annotation Packages?}
\begin{figure}[ht]
 \centering
  \includegraphics[width=4in,height=3in]{databaseTypesSuggestion}
\end{figure}
\end{frame}



\end{document}

