%\VignetteIndexEntry{Supplement to A tutorial on how to analyze ChIP-chip readouts using Bioconductor} %\VignetteDepends{Ringo, biomaRt, topGO} %\VignetteKeywords{microarray ChIP-chip NimbleGen nimblegen} %\VignettePackage{ccTutorial} % name of package %%%% HEAD SECTION: START EDITING BELOW %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% To compile the .Rnw file into a .tex file and figures: %% library("weaver");Sweave("ccTutorialSupplement.Rnw", driver=weaver()) %% then run "make supp" for producing the PDF \documentclass[11pt, a4paper, fleqn]{article} \usepackage{geometry}\usepackage{color} \definecolor{darkblue}{rgb}{0.0,0.0,0.75} \usepackage[% baseurl={http://www.bioconductor.org},% pdftitle={Supplement to A tutorial on how to analyze ChIP-chip readouts using Bioconductor},% pdfauthor={Joern Toedling},% pdfsubject={Vignette},% pdfkeywords={Bioconductor},% pagebackref,bookmarks,%colorlinks,linkcolor=darkblue,citecolor=darkblue,% filecolor=darkblue,urlcolor=darkblue,pagecolor=darkblue,% raiselinks,plainpages,pdftex]{hyperref} \usepackage{amsmath,a4,t1enc, graphicx} %\usepackage{natbib} %\bibpunct{(}{)}{;}{a}{,}{,} \usepackage{verbatim} \usepackage{subfigure} \parindent 0mm \parskip 2ex plus0.5ex minus0.3ex \newcommand{\Robject}[1]{{\texttt{#1}}} \newcommand{\Rfunction}[1]{{\texttt{#1}}} \newcommand{\Rpackage}[1]{{\textit{#1}}} \newcommand{\Rclass}[1]{{\textit{#1}}} \newcommand{\Rmethod}[1]{{\textit{#1}}} \newcommand{\Rfunarg}[1]{{\texttt{#1}}} \newcommand{\phead}[1]{{\flushleft \sf \small \textbf{#1} \quad}} \newcommand{\todo}{{\textbf{TO DO:} \quad}} \renewcommand{\thetable}{S\arabic{table}} \renewcommand{\thefigure}{S\arabic{figure}} \newcommand{\myincfig}[3]{% \begin{figure}[htb] \begin{center} \includegraphics[width=#2]{#1} \caption{\label{#1}\textit{#3}} \end{center} \end{figure} } \addtolength{\textwidth}{2cm} \addtolength{\oddsidemargin}{-1cm} \addtolength{\evensidemargin}{-1cm} \addtolength{\textheight}{2cm} \addtolength{\topmargin}{-1cm} \addtolength{\skip\footins}{1cm} %%%%%%% START EDITING HERE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{document} \SweaveOpts{eps=false, include=FALSE} % produce no 'eps' figures \title{Supplement: A tutorial on how to analyze ChIP-chip readouts using Bioconductor} \author{Joern Toedling, Wolfgang Huber} %\date{} \maketitle \tableofcontents <>= options(length=60) set.seed(123) @ This is only a placeholder. The real vignette has been pre-created, since it takes quite some time to process. \section*{Software versions} This supplement was generated using the following package versions: <>= toLatex(sessionInfo()) @ \end{document}