%\VignetteIndexEntry{Overview of copy number vignettes}
\newcommand{\oligo}{\Rpackage{oligo }}

\title{Overview of vignettes for copy number estimation}
\author{Rob Scharpf}

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

 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       &  genomewidesnp5crlmml, genomewidesnp6Crlmm  &  Preprocessing, genotyping, CN estimation\\
 IlluminaPreprocessCN    &  Illumina  &  several$^\dagger$ &
                  Preprocessing, genotyping, CN estimation\\ \hline
\caption{\label{overview} Vignettes for copy number
  estimation. $^\dagger$ See \texttt{annotationPackages()} for a
  complete listing of supported Illumina/Affy platforms}

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{}