%\VignetteIndexEntry{crlmmDownstream}
%\VignetteKeywords{copy number, genotype, SNP}
%\VignettePackage{VanillaICE}
\documentclass{article}
\usepackage{amsmath}
\usepackage{graphicx}
\usepackage[numbers]{natbib}
\usepackage{color}
\usepackage[margin=1in]{geometry}

\newcommand{\scscst}{\scriptscriptstyle}
\newcommand{\scst}{\scriptstyle}
\newcommand{\Rpackage}[1]{\textit{#1}}
\newcommand{\Rfunction}[1]{\texttt{#1}}
\newcommand{\Robject}[1]{\texttt{#1}}
\newcommand{\Rclass}[1]{\texttt{#1}}
\newcommand{\R}{\textsf{R}}
\newcommand{\hmmoptions}{\Robject{HmmOptions}}
\newcommand{\hmmparam}{\Robject{HmmParameter}}
\newcommand{\crlmm}{\Rpackage{crlmm}}
\newcommand{\oligo}{\Rpackage{oligo}}

\title{Integration with the crlmm package for copy number inference}
\author{Robert Schgarpf}

\begin{document}

\maketitle

We load a portion of chromosome 8 from 2 HapMap samples that were
processed using the \Rpackage{crlmm} package.

<<loadData>>=
library(oligoClasses)
library(VanillaICE)
library2(crlmm)
library2(SNPchip)
library2(IRanges)
data(cnSetExample, package="crlmm")
@

The data \Robject{cnSetExample} is an object of class \Rclass{CNSet}.
We coerce the \Rclass{CNSet} objectf to an object of class
\Rclass{oligoSnpSet} containing log R ratios and B allele frequencies.

<<coerce2OligoSnpSet>>=
oligoSet <- as(cnSetExample, "oligoSnpSet")
@

Next, we fit a 6-state hidden markov model from estimates of the B
allele frequency and log R ratios.

<<hmm>>=
res <- hmm(oligoSet, p.hom=0, TAUP=1e8)
@

The \texttt{TAUP} parameter scales the transition probability matrix.
Larger values of \texttt{TAUP} makes it more expensive to transition
from the normal copy number state to states with altered copy
number. In the following code chunk, we use a lattice multi-panel
display to plot each of the altered stated.  We frame each alteration
by plotting a genomic interval of 200kb on each side (using the
\texttt{frame=200e3} argument):

<<xyplot>>=
rd <- res[!state(res)%in%c(3,4), ]
fig <- SNPchip:::xyplotLrrBaf(rd[1:2, ], oligoSet,
			      frame=200e3,
			      panel=SNPchip:::xypanelBaf,
			      scales=list(x="free"),
			      par.strip.text=list(cex=0.6),
			      pch=".")
@

<<latticeFig, echo=false, fig=TRUE, include=FALSE,width=8, height=7>>=
print(fig)
@

\begin{figure}[t]
  \includegraphics[width=0.9\textwidth]{crlmmDownstream-latticeFig}
  \caption{\label{fig:chr8} Plot of log R ratios (grey) and B allele
    frequencies (blue). The B allele frequencies have a range of 0-1
    and were rescaled for ease of viewing alongside the log R
    ratios. Each panel displays one region with a copy number
    alteration predicted from the 6-state HMM.}
\end{figure}

\end{document}