Browse code

merge collab branch

* collab:
update vignettes/Makefile
update .gitignore
update table in CopyNumberViewiew
bump dependency on oligoClasses version
Update alias for "[" method for PredictionRegion objects
Replaced CopyNumberOverview and Infrastructure vignettes with those in the release branch. The versions in release have removed AffymetrixPreprocessCN, which is no longer available

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@71322 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/11/2012 04:49:34
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@@ -42,42 +42,18 @@ appropriate.
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 \begin{center}
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 \begin{tabular}{|lp{1.2in}p{1.5in}p{2in}|}
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 \hline
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- Vignette                &  Platform            &  Annotation package                        &  Scope                                               \\
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-\hline
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-Infrastructure          & Affy/Illumina                    &
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-&  The CNSet container / large data support using the \Rpackage{ff} package            \\
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- AffymetrixPreprocessCN  &  Affy 5.0, 6.0       &  genomewidesnp5Crlmm, genomewidesnp6Crlmm  &  Preprocessing and genotyping                        \\
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- IlluminaPreprocessCN    &  Illumina  &  several$^\dagger$                                   &  Preprocessing and genotyping                        \\
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- copynumber              &  Affy/Illumina       &  N/A                                       &  raw copy number estimates                           \\
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-% SmoothingRawCN          &  Affy/Illumina       &  N/A                                       &  smoothing via segmentation or hidden Markov models  \\
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-\hline
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+ Vignette  &  Platform &  Annotation package  &  Scope  \\\hline
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+Infrastructure   & Affy/Illumina  & &  The CNSet container / large data support using the \Rpackage{ff} package            \\
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+ AffyGW  &  Affy 5.0, 6.0       &  genomewidesnp5crlmml, genomewidesnp6Crlmm  &  Preprocessing, genotyping, CN estimation\\
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+ IlluminaPreprocessCN    &  Illumina  &  several$^\dagger$ &
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+                  Preprocessing, genotyping, CN estimation\\ \hline
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 \end{tabular}
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 \end{center}
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 \caption{\label{overview} Vignettes for copy number
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-  estimation. $^\dagger$ Annotation packages available for the
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-  Illumina platform include  \Rpackage{human370v1cCrlmm}, \Rpackage{human370quadv3cCrlmm},
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-  \Rpackage{human550v3bCrlmm}, \Rpackage{human650v3aCrlmm}, \Rpackage{human610quadv1bCrlmm},
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-  \Rpackage{human660quadv1aCrlmm}, \Rpackage{human1mduov3bCrlmm}, and \Rpackage{humanomni1quadv1bCrlmm}}
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+  estimation. $^\dagger$ See \texttt{annotationPackages()} for a
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+  complete listing of supported Illumina/Affy platforms}
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 \end{table}
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-%We make use of the \R{} package \Rpackage{cacheSweave} for cacheing
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-%code chunks that are computationally intensive.  In addition, we
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-%indicate that the cached files should be stored in the directory
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-%\verb+outdir+.
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-
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-In general, the workflow is
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-\begin{enumerate}
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-\item preprocess and genotype the arrays
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-  (\verb+AffymetrixPreprocessCN+ for Affymetrix and
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-  \verb+IlluminaPreprocessCN+ vignettes for Illumina)
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-\item copy number estimation (\verb+copynumber+ vignette)
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-%\item inferring regions of copy number gain and loss
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-%  (\verb+SmoothingRawCN+ vignette)
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-\end{enumerate}
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-%The \verb+SmoothingRawCN+ vignette illustrates one approach for
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-%interfacing with packages such as \Rpackage{DNAcopy} and
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-%\Rpackage{VanillaICE} for identifying regions of copy number gain or
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-%loss.
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 The \verb+Infrastructure+ vignette provides additional details on the
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 \Rclass{CNSet} container used to organize the processed data as well
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 as a brief discussion regarding large data support through the \ff{}
Browse code

Merge branch 'collab'

* collab:
fixing vignettes dir
fixing vignettes dir
removing old vignettes
removing old vignettes
Adding GGdata to suggests
Fixed vignette for genotyping + association; Moved oligoClasses back to Depends b/c final users do need access to calls()/confs() when using crlmm()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@64350 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 23/03/2012 17:35:35
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+%\VignetteIndexEntry{Overview of copy number vignettes}
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+%\VignetteDepends{}
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+%\VignetteKeywords{}
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+%\VignettePackage{crlmm}
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+\documentclass{article}
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+\usepackage{graphicx}
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+\usepackage{natbib}
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+\usepackage{url}
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+\newcommand{\Rfunction}[1]{{\texttt{#1}}}
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+\newcommand{\Rmethod}[1]{{\texttt{#1}}}
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+\newcommand{\Rcode}[1]{{\texttt{#1}}}
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+\newcommand{\Robject}[1]{{\texttt{#1}}}
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+\newcommand{\Rpackage}[1]{{\textsf{#1}}}
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+\newcommand{\Rclass}[1]{{\textit{#1}}}
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+\newcommand{\oligo}{\Rpackage{oligo }}
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+\newcommand{\R}{\textsf{R}}
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+\newcommand{\crlmm}{\Rpackage{crlmm}}
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+\newcommand{\ff}{\Rpackage{ff}}
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+\usepackage[margin=1in]{geometry}
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+
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+\begin{document}
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+\title{Overview of vignettes for copy number estimation}
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+\date{\today}
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+\author{Rob Scharpf}
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+\maketitle
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+
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+The workflow for copy number analyses in the \crlmm{} package includes
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+preprocessing and genotyping of the raw intensities followed by
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+estimation of parameters for copy number estimation using
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+\Rfunction{crlmmCopynumber}.  Supported platforms are those for which
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+a corresponding annotation package is available.  Table \ref{overview}
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+provides an overview of the available vignettes pertaining to copy
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+number estimation.  These vignettes are located in the
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+\verb+inst/scripts+ subdirectory of the \crlmm{} package. HapMap
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+datasets are used to illustrate the workflow and are not provided as
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+part of the \crlmm{} package.  Users wishing to reproduce the analysis
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+should download the HapMap CEL files (Affymetrix) or the \verb+idat+
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+files (Illumina) and modify the paths to the raw data files as
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+appropriate.
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+
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+\begin{table}[h!]
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+\begin{center}
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+\begin{tabular}{|lp{1.2in}p{1.5in}p{2in}|}
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+\hline
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+ Vignette                &  Platform            &  Annotation package                        &  Scope                                               \\
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+\hline
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+Infrastructure          & Affy/Illumina                    &
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+&  The CNSet container / large data support using the \Rpackage{ff} package            \\
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+ AffymetrixPreprocessCN  &  Affy 5.0, 6.0       &  genomewidesnp5Crlmm, genomewidesnp6Crlmm  &  Preprocessing and genotyping                        \\
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+ IlluminaPreprocessCN    &  Illumina  &  several$^\dagger$                                   &  Preprocessing and genotyping                        \\
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+ copynumber              &  Affy/Illumina       &  N/A                                       &  raw copy number estimates                           \\
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+% SmoothingRawCN          &  Affy/Illumina       &  N/A                                       &  smoothing via segmentation or hidden Markov models  \\
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+\hline
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+\end{tabular}
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+\end{center}
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+\caption{\label{overview} Vignettes for copy number
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+  estimation. $^\dagger$ Annotation packages available for the
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+  Illumina platform include  \Rpackage{human370v1cCrlmm}, \Rpackage{human370quadv3cCrlmm},
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+  \Rpackage{human550v3bCrlmm}, \Rpackage{human650v3aCrlmm}, \Rpackage{human610quadv1bCrlmm},
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+  \Rpackage{human660quadv1aCrlmm}, \Rpackage{human1mduov3bCrlmm}, and \Rpackage{humanomni1quadv1bCrlmm}}
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+\end{table}
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+
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+%We make use of the \R{} package \Rpackage{cacheSweave} for cacheing
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+%code chunks that are computationally intensive.  In addition, we
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+%indicate that the cached files should be stored in the directory
66
+%\verb+outdir+.
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+
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+In general, the workflow is
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+\begin{enumerate}
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+\item preprocess and genotype the arrays
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+  (\verb+AffymetrixPreprocessCN+ for Affymetrix and
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+  \verb+IlluminaPreprocessCN+ vignettes for Illumina)
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+\item copy number estimation (\verb+copynumber+ vignette)
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+%\item inferring regions of copy number gain and loss
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+%  (\verb+SmoothingRawCN+ vignette)
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+\end{enumerate}
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+%The \verb+SmoothingRawCN+ vignette illustrates one approach for
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+%interfacing with packages such as \Rpackage{DNAcopy} and
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+%\Rpackage{VanillaICE} for identifying regions of copy number gain or
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+%loss.
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+The \verb+Infrastructure+ vignette provides additional details on the
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+\Rclass{CNSet} container used to organize the processed data as well
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+as a brief discussion regarding large data support through the \ff{}
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+package.
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+
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+\end{document}
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