%\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                                               \\
Infrastructure          & Affy/Illumina                    &
&  The CNSet container / large data support using the \Rpackage{ff} package            \\
 AffymetrixPreprocessCN  &  Affy 5.0, 6.0       &  genomewidesnp5Crlmm, genomewidesnp6Crlmm  &  Preprocessing and genotyping                        \\
 IlluminaPreprocessCN    &  Illumina  &  several$^\dagger$                                   &  Preprocessing and genotyping                        \\
 copynumber              &  Affy/Illumina       &  N/A                                       &  raw copy number estimates                           \\
% SmoothingRawCN          &  Affy/Illumina       &  N/A                                       &  smoothing via segmentation or hidden Markov models  \\
\caption{\label{overview} Vignettes for copy number
  estimation. $^\dagger$ Annotation packages available for the
  Illumina platform include  \Rpackage{human370v1cCrlmm}, \Rpackage{human370quadv3cCrlmm},
  \Rpackage{human550v3bCrlmm}, \Rpackage{human650v3aCrlmm}, \Rpackage{human610quadv1bCrlmm},
  \Rpackage{human660quadv1aCrlmm}, \Rpackage{human1mduov3bCrlmm}, and \Rpackage{humanomni1quadv1bCrlmm}}

%We make use of the \R{} package \Rpackage{cacheSweave} for cacheing
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In general, the workflow is
\item preprocess and genotype the arrays
  (\verb+AffymetrixPreprocessCN+ for Affymetrix and
  \verb+IlluminaPreprocessCN+ vignettes for Illumina)
\item copy number estimation (\verb+copynumber+ vignette)
%\item inferring regions of copy number gain and loss
%  (\verb+SmoothingRawCN+ vignette)
%The \verb+SmoothingRawCN+ vignette illustrates one approach for
%interfacing with packages such as \Rpackage{DNAcopy} and
%\Rpackage{VanillaICE} for identifying regions of copy number gain or
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{}