%\VignetteIndexEntry{A tutorial on how to analyze ChIP-chip readouts using Bioconductor} %\VignetteDepends{ } %\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("ccTutorial.Rnw", driver=weaver()) \documentclass[11pt, a4paper, fleqn]{article} \usepackage{geometry} \usepackage[% baseurl={http://www.bioconductor.org},% pdftitle={Analyzing ChIP-chip data 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{verbatim} \usepackage{subfigure} \usepackage{boxedminipage} \parindent0mm \parskip2ex 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}} \newcommand{\myincfig}[3]{% \begin{figure}[tbh] \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} \addtolength{\fboxsep}{8pt} %%%%%%% START EDITING HERE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{document} \SweaveOpts{eps=false,include=FALSE,keep.source=TRUE} \title{Analyzing ChIP-chip data using Bioconductor} \author{Joern Toedling, Wolfgang Huber} \maketitle <>= options(length=55, digits=3) set.seed(1) @ This is only a placeholder. The real vignette has been pre-created since it takes quite some time to process. \section*{Software versions} This tutorial was generated using the following package versions: <>= toLatex(sessionInfo()) @ \end{document}