* 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{}
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* 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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new file mode 100644 |
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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 |
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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{}
|
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+package. |
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+ |
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+\end{document}
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\ No newline at end of file |