* 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
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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{} |
* 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
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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}|} |
|
44 |
+\hline |
|
45 |
+ Vignette & Platform & Annotation package & Scope \\ |
|
46 |
+\hline |
|
47 |
+Infrastructure & Affy/Illumina & |
|
48 |
+& The CNSet container / large data support using the \Rpackage{ff} package \\ |
|
49 |
+ AffymetrixPreprocessCN & Affy 5.0, 6.0 & genomewidesnp5Crlmm, genomewidesnp6Crlmm & Preprocessing and genotyping \\ |
|
50 |
+ IlluminaPreprocessCN & Illumina & several$^\dagger$ & Preprocessing and genotyping \\ |
|
51 |
+ copynumber & Affy/Illumina & N/A & raw copy number estimates \\ |
|
52 |
+% 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 |
|
57 |
+ estimation. $^\dagger$ Annotation packages available for the |
|
58 |
+ Illumina platform include \Rpackage{human370v1cCrlmm}, \Rpackage{human370quadv3cCrlmm}, |
|
59 |
+ \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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+ |
|
63 |
+%We make use of the \R{} package \Rpackage{cacheSweave} for cacheing |
|
64 |
+%code chunks that are computationally intensive. In addition, we |
|
65 |
+%indicate that the cached files should be stored in the directory |
|
66 |
+%\verb+outdir+. |
|
67 |
+ |
|
68 |
+In general, the workflow is |
|
69 |
+\begin{enumerate} |
|
70 |
+\item preprocess and genotype the arrays |
|
71 |
+ (\verb+AffymetrixPreprocessCN+ for Affymetrix and |
|
72 |
+ \verb+IlluminaPreprocessCN+ vignettes for Illumina) |
|
73 |
+\item copy number estimation (\verb+copynumber+ vignette) |
|
74 |
+%\item inferring regions of copy number gain and loss |
|
75 |
+% (\verb+SmoothingRawCN+ vignette) |
|
76 |
+\end{enumerate} |
|
77 |
+%The \verb+SmoothingRawCN+ vignette illustrates one approach for |
|
78 |
+%interfacing with packages such as \Rpackage{DNAcopy} and |
|
79 |
+%\Rpackage{VanillaICE} for identifying regions of copy number gain or |
|
80 |
+%loss. |
|
81 |
+The \verb+Infrastructure+ vignette provides additional details on the |
|
82 |
+\Rclass{CNSet} container used to organize the processed data as well |
|
83 |
+as a brief discussion regarding large data support through the \ff{} |
|
84 |
+package. |
|
85 |
+ |
|
86 |
+\end{document} |
|
0 | 87 |
\ No newline at end of file |