vignettes/CopyNumberOverview.Rnw
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 %\VignetteIndexEntry{Overview of copy number vignettes}
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 %\VignettePackage{crlmm}
 \documentclass{article}
 \usepackage{graphicx}
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 \begin{document}
 \title{Overview of vignettes for copy number estimation}
 \date{\today}
 \author{Rob Scharpf}
 \maketitle
 
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 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.
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 \begin{table}[h!]
 \begin{center}
 \begin{tabular}{|lp{1.2in}p{1.5in}p{2in}|}
 \hline
  Vignette                &  Platform            &  Annotation package                        &  Scope                                               \\
 \hline
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 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
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 \hline
 \end{tabular}
 \end{center}
 \caption{\label{overview} Vignettes for copy number
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   estimation. $^\dagger$ See \texttt{annotationPackages()} for a
   complete listing of supported Illumina/Affy platforms}
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 \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}