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  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-12-28 17:17:25 UTC
  • mfrom: (1.1.2)
  • Revision ID: package-import@ubuntu.com-20131228171725-polmzo8go4m371c6
Tags: 2.4.1-1
* New upstream version
* debian/rules: Remove useless creation of ${R-Depends}
* debian/control: Versioned Build-Depends: r-base-dev (>= 3.0)
* debian/README.test: add hint how to test the package

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inst/reports/runReport.Rnw
 
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
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%\SweaveOpts{prefix.string=graphics/plot}
 
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\documentclass[10pt]{article}
 
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\usepackage{amsmath}
 
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\usepackage[authoryear,round]{natbib}
 
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\usepackage{hyperref}
 
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\hypersetup{
 
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    colorlinks,
 
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    citecolor=black,
 
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    filecolor=black,
 
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    linkcolor=red,
 
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    urlcolor=black
 
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}
 
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\usepackage{theorem}
 
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\usepackage{float}
 
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\usepackage{ifthen}
 
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\usepackage[OT1]{fontenc}
 
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\newcommand{\R}{{\textsf{R}}}
 
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\newcommand{\code}[1]{{\texttt{#1}}}
 
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\newcommand{\term}[1]{{\emph{#1}}}
 
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\newcommand{\Rpackage}[1]{\textsf{#1}}
 
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\newcommand{\Rfunction}[1]{\texttt{#1}}
 
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\newcommand{\Robject}[1]{\texttt{#1}}
 
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\newcommand{\Rclass}[1]{{\textit{#1}}}
 
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\newcommand{\Rmethod}[1]{{\textit{#1}}}
 
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\newcommand{\Rfunarg}[1]{{\textit{#1}}}
 
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\bibliographystyle{plainnat}
 
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\title{cummeRbund Run Report}
 
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\date{}
 
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\begin{document}
 
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<<init, echo=FALSE>>=
 
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options(width=65)
 
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library(cummeRbund)
 
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library(xtable)
 
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cuff<-readCufflinks(dir="../",dbfile="cuffData.db")
 
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@ 
 
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\maketitle
 
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\tableofcontents
 
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\section{Run Parameters}
 
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<<>>=
 
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runInfo(cuff)
 
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@
 
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\section{Samples}
 
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\subsection{Condition Information}
 
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\subsection{Replicate Information}
 
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<<results=tex>>=
 
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xtable(replicates(cuff),caption="Replicate information")
 
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@
 
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\section{Gene information}
 
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\section{Model statistics}
 
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\section{Differential Expression Analysis}
 
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\section{Condition Specificity}
 
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%Put \subsection loop here for specificity on each condition including top genes?
 
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\clearpage
 
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\section{Session info}
 
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<<label=close_connection,echo=FALSE>>=
 
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end<-sqliteCloseConnection(cuff@DB)
 
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@
 
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<<session>>=
 
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sessionInfo()
 
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@
 
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\end{document}