@@ -5,6 +5,7 @@

 \documentclass{article}

 \usepackage{graphicx}

 \usepackage{natbib}

+\usepackage{url}

 \newcommand{\Rfunction}[1]{{\texttt{#1}}}

 \newcommand{\Rmethod}[1]{{\texttt{#1}}}

 \newcommand{\Rcode}[1]{{\texttt{#1}}}

@@ -33,8 +34,11 @@ options(continue=" ", width=70)

 \begin{abstract}

   This vignette estimates copy number for HapMap samples on the

-  Affymetrix 6.0 platform.  See \citep{Scharpf2010} for additional

-  details.

+  Affymetrix 6.0 platform.  See \citep{Scharpf2010} for details

+  regarding the methodology implemented in \crlmm{}.  In addition, a

+  compendium describing copy number analysis using the \crlmm{}

+  package is available from the author's website:

+  \url{http://www.biostat.jhsph.edu/~rscharpf/crlmmCompendium/index.html}.

 \end{abstract}

@@ -6,6 +6,7 @@

 \alias{phiA}

 \alias{phiB}

 \alias{totalCopynumber}

+\alias{rawCopynumber}

 \title{

@@ -28,6 +29,7 @@ nuB(object)

 phiA(object)

 phiB(object)

 totalCopynumber(object,...)

+rawCopynumber(object,...)

 }

 \arguments{

@@ -64,7 +66,7 @@ totalCopynumber(object,...)

 	CA and CB return matrices of allele-specific copy number.  

-	totalCopynumber returns a matrix of CA+CB.

+	totalCopynumber (or rawCopynumber) returns a matrix of CA+CB.

 }