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\begin{document}
\title{Overview of vignettes for copy number estimation}
\date{\today}
\author{Rob Scharpf}
\maketitle

The workflow for copy number analyses in the \crlmm{} package includes
preprocessing and genotyping of the raw intensities followed by
estimation of parameters for copy number estimation using
\Rfunction{crlmmCopynumber}.  Supported platforms are those for which
a corresponding annotation package is available.  Table \ref{overview}
provides an overview of the available vignettes pertaining to copy
number estimation.  These vignettes are located in the
\verb+inst/scripts+ subdirectory of the \crlmm{} package. HapMap
datasets are used to illustrate the workflow and are not provided as
part of the \crlmm{} package.  Users wishing to reproduce the analysis
should download the HapMap CEL files (Affymetrix) or the \verb+idat+
files (Illumina) and modify the paths to the raw data files as
appropriate.

\begin{table}[h!]
\begin{center}
\begin{tabular}{|lp{1.2in}p{1.5in}p{2in}|}
\hline
 Vignette                &  Platform            &  Annotation package                        &  Scope                                               \\
\hline
Infrastructure          & Affy/Illumina                    & &  The CNSet container / large data support using the \Rpackage{ff} package            \\
 AffyGW  &  Affy 5.0, 6.0       &  genomewidesnp5Crlmm, genomewidesnp6Crlmm  &  Preprocessing, genotyping, CN estimation\\
 IlluminaPreprocessCN    &  Illumina  &  several$^\dagger$ &  Preprocessing, genotyping, CN estimation
\hline
\end{tabular}
\end{center}
\caption{\label{overview} Vignettes for copy number
  estimation. $^\dagger$ See \texttt{annotationPackages()} for a
  complete listing of supported Illumina/Affy platforms}
\end{table}

The \verb+Infrastructure+ vignette provides additional details on the
\Rclass{CNSet} container used to organize the processed data as well
as a brief discussion regarding large data support through the \ff{}
package.

\end{document}