%\VignetteIndexEntry{DmelSGI}
%\VignettePackage{DmelSGI}
%\VignetteEngine{knitr::knitr}
\documentclass[10pt,a4paper,oneside]{article}

\usepackage{amsfonts,amsmath,amstext,amssymb,amscd}
% \usepackage{subfig}

\newenvironment{packeditemize}{
\begin{itemize}
  \setlength{\itemsep}{1pt}
  \setlength{\parskip}{0pt}
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}{\end{itemize}}

\newenvironment{packedenumerate}{
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<<DmelSGIstyle, echo=FALSE, results="asis">>=
  BiocStyle::latex(bibstyle="apalike")
@

\bioctitle[A Map of Directional Genetic Interactions in a Metazoan Cell, 
Fischer et al., 2015]{{\Large\color{black} Experimental data and documented source code for the paper}\\\\
               A Map of Directional Genetic Interactions in a Metazoan Cell\\[0.5em]
               \Large\textit{\color{black}Bernd Fischer, Thomas Sandmann, Thomas Horn, Maximilian
               Billmann, Varun Chaudhary, Wolfgang Huber, and Michael Boutros\\
               eLife, 4, 2015}}

\author{Bernd Fischer\thanks{\email{b.fischer@dkfz.de}}\\
German Cancer Research Center (DKFZ), Heidelberg, Germany}

<<DmelSGIopts,include=FALSE>>=
library(knitr)
opts_chunk$set(concordance=TRUE, 
               resize.width="0.5\\textwidth",
               dev=c('pdf','png'),
               cache=TRUE,
               tidy = FALSE)
@

\begin{document}

\maketitle
\tableofcontents


\section{Introduction}
This document is associated with the \Bioconductor{} package \Rpackage{DmelSGI},
which contains the data and the \R{} code for the statistical analysis
presented in the paper \\\\
\begin{center}
\begin{minipage}[t]{0.96\textwidth}
\textit{A Map of Directional Genetic Interactions in a Metazoan Cell}\\
Bernd Fischer, Thomas Sandmann, Thomas Horn, Maximilian
               Billmann, Varun Chaudhary, Wolfgang Huber, and Michael Boutros\\
               eLife, in press, http://www.elifesciences.org.\\
\end{minipage}
\end{center}

In Section~\ref{secDataAccess}, the access to the data is described. 
% Section~\ref{Figures} shows the figures from the original
% publication and links each figure to one of the subsequent sections,
% which describe the statistical analyses in the order in which they
% were executed. 
The \R{} code within each section can be executed
independently of the other sections.  Intermediate results from each
section are available in the form of \R{} data objects.

To install the \Biocexptpkg{DmelSGI}, please start a current version of
\R{} and type
<<DmelSGIinstallation,eval=FALSE>>=
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("DmelSGI")
@

Some convenience functions for calling sub-vignettes.
<<DmelSGIfunctions>>=
fpath <- function(d) { file.path(opts_knit$get("output.dir"), "result", d,"") }
@ 

<<DmelSGIdataAccess, child=file.path('src/sec01_dataAccess.Rnw'), eval=TRUE>>=
@ 

<<DmelSGIreanalysisOfHornEtAl, fig.path=fpath("ReanalysisOfHornEtAl"),child=file.path('src','sec02_ReanalysisOfHornEtAl.Rnw'), eval=TRUE>>=
@

<<DmelSGIqueryGeneSelection, fig.path=fpath("QueryGeneSelection"), child=file.path('src','sec03_QueryGeneSelection.Rnw'), eval=TRUE>>=
@

<<DmelSGIimageProcessing, fig.path=fpath("ImageProcessing"), child=file.path('src','sec04_ImageProcessing.Rnw'), eval=TRUE>>=
@

<<DmelSGIqualityControl, fig.path=fpath("QualityControl"), child=file.path('src','sec05_QualityControl.Rnw'), eval=TRUE>>=
@

<<DmelSGIfeatureSelection, fig.path=fpath("FeatureSelection"), child=file.path('src','sec06_FeatureSelection.Rnw'), eval=TRUE>>=
@

<<DmelSGIpairwiseInteractionScores, fig.path=fpath("PairwiseInteractionScores"), child=file.path('src','sec07_PairwiseInteractionScores.Rnw'), eval=TRUE>>=
@

<<DmelSGIgeneticInteractionCube, fig.path=fpath("GeneticInteractionCube"), child=file.path('src','sec08_GeneticInteractionCube.Rnw'), eval=TRUE>>=
@

<<DmelSGIgeneticInteractionLandscape, fig.path=fpath("GeneticInteractionLandscape"), child=file.path('src','sec09_GeneticInteractionLandscape.Rnw'), eval=TRUE>>=
@

<<DmelSGIdirectionalInteractions, fig.path=fpath("DirectionalInteractions"), child=file.path('src','sec10_directionalInteractions.Rnw'), eval=TRUE>>=
@

\section{Session info}
Here is the output of \Rfunction{sessionInfo} on the system on which this 
document was compiled:
<<DmelSGIsessioninfo>>=
sessionInfo()
@

\nocite{horn2011mapping}

\bibliography{literature}

\end{document}