Browse code

Add link to compendium in copy number vignette.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@53579 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 10/03/2011 19:31:02
Showing2 changed files

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@@ -5,6 +5,7 @@
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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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@@ -33,8 +34,11 @@ options(continue=" ", width=70)
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 \begin{abstract}
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   This vignette estimates copy number for HapMap samples on the
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-  Affymetrix 6.0 platform.  See \citep{Scharpf2010} for additional
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-  details.
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+  Affymetrix 6.0 platform.  See \citep{Scharpf2010} for details
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+  regarding the methodology implemented in \crlmm{}.  In addition, a
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+  compendium describing copy number analysis using the \crlmm{}
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+  package is available from the author's website:
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+  \url{http://www.biostat.jhsph.edu/~rscharpf/crlmmCompendium/index.html}.
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 \end{abstract}
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@@ -6,6 +6,7 @@
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 \alias{phiA}
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 \alias{phiB}
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 \alias{totalCopynumber}
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+\alias{rawCopynumber}
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 \title{
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@@ -28,6 +29,7 @@ nuB(object)
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 phiA(object)
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 phiB(object)
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 totalCopynumber(object,...)
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+rawCopynumber(object,...)
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 }
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 \arguments{
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@@ -64,7 +66,7 @@ totalCopynumber(object,...)
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 	CA and CB return matrices of allele-specific copy number.  
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-	totalCopynumber returns a matrix of CA+CB.
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+	totalCopynumber (or rawCopynumber) returns a matrix of CA+CB.
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 }
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