RIntro.Rnw

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% Author, Title, etc.
\title[R Introduction]
{%
  An Introduction to R 
}

\author[L. Gatto]
{
  Laurent Gatto \\
  \scriptsize \url{lg390@cam.ac.uk}
}

%% \institute[CCP]
%% {
%% %   \inst{1}%
%%   Cambridge System Biology Centre\\
%%   University of Cambridge \\
%% }

\date[]
{
  \textbf{Microarray Analysis using \R and Bioconductor}\\
  diXa Training --  28$^{th}$ Jan 2014
}


\pgfdeclareimage[height=.7cm]{uc-logo}{./Figures/uc-logo}
\pgfdeclareimage[height=.7cm]{ebi-logo}{./Figures/EMBLEBIlogo}
% \logo{\pgfuseimage{uc-logo}}


\AtBeginSection[] % Do nothing for \section*
{
\begin{frame}<beamer>
\frametitle{Plan}
\tableofcontents[currentsection]
\end{frame}
}


% The main document

\begin{document}

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\begin{frame}
  \titlepage
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%% Table of contents                                           %% 
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\begin{frame}{Plan}
  \footnotesize
  \tableofcontents
\end{frame}

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<<echo=FALSE, message=FALSE>>=
library(Biobase)
data(sample.ExpressionSet)
@ 

\input{Sec-AboutR.tex}

\input{Sec-IntroR.tex}

\input{Sec-DataTypes1.tex}

\input{Sec-DataTypes2.tex}

\input{Sec-UseCase.tex}

\input{Sec-Packages.tex}

\input{Sec-RBioc.tex}

\input{Sec-objects.tex}

\input{Sec-BiocCase.tex}

%% \input{Sec-Plotting.tex}

%% \input{Sec-Programming.tex}


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%% section                                                     %% 
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\begin{frame}{References}
  \begin{block}{General}
    \begin{itemize}
    \item W. N. Venables, D. M. Smith and the R Development Core Team, 
      An Introduction to R (get it with \Rfunction{help.start()})
    \item R. Gentleman, R Programming for Bioinformatics, CRC Press, 2008
    \item Plenty of free documentation on the \R web page and elsewhere.
    \end{itemize}
  \end{block}
  \begin{block}{Bioconductor}
    \begin{itemize}  
    \item Gentleman et al., 
      \textit{Bioconductor: open software development for computational biology and bioinformatics},      
      Genome Biol. 2004; 5:(10)R80
    \item \textit{Bioconductor Case Studies}, 2008, Springer.
    \end{itemize}
  \end{block}
\end{frame}

\begin{frame}{References}
  \begin{block}{Plotting}
    \begin{itemize}
    \item We have covered base graphics, not \Rpackage{lattice} and \Rpackage{ggplot2}.
    \item Lattice: Multivariate Data Visualization with R, Deepayan Sarkar (2008)
    \item ggplot2: Elegant Graphics for Data Analysis, Hadley Wickham (2010)
    \item \url{http://gallery.r-enthusiasts.com/allgraph.php}
    \item R Graphics manual: \url{http://rgm3.lab.nig.ac.jp/RGM/r_image_list}
    \item \url{http://www.cookbook-r.com/Graphs/} (ggplot2)
    \end{itemize}
  \end{block}
\end{frame}


\begin{frame}[fragile]
<<sessioninfo, results='asis'>>=
toLatex(sessionInfo())
@   
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\begin{frame}
  \vspace{2cm}
  \begin{itemize}
  \item Parts of these slides are based on the
    \textit{Beginners guide to solving biological problems in \texttt{R}} course\footnote{%%
      \url{http://www.training.cam.ac.uk/gsls/course/gsls-rintro}}, University of Cambridge.
  \item This work is licensed under a CC BY-SA 3.0 License 
  \item Course web page: \url{https://github.com/lgatto/TeachingMaterial}
  \end{itemize}
  \vspace{.7cm}
  \begin{center}
  \textbf{Thank you for your attention}

  \vspace{1cm}
  \includegraphics[width=2cm]{./Figures/cc-by-sa.png}
  \end{center}
  

\end{frame}

\end{document}