%\VignetteIndexEntry{1. Primer}
%\VignetteKeywords{Preprocessing, Affymetrix}
%\VignetteDepends{BAC}
%\VignettePackage{BAC}

\documentclass{article}
\usepackage{hyperref}

\begin{document}

\title{Bayesian Analysis of ChIP-chip\\
The BAC package}
\author{Raphael Gottardo}
\maketitle

\textnormal {\normalfont}

\tableofcontents
\newpage

\part{Licensing}

This software is distributed under the Artistic License 2.0. In addition, we would appreciate if you cite the following papers when using this software for publication. 
\begin{itemize}
\item[]W. E. Johnson, Li, W., Meyer, C. A., Gottardo, R., Carroll, J. S., Brown, M., and Liu, X. S. (2006). Model-based analysis of tiling-arrays for ChIP-chip. PNAS 103:12457-12462.
\item[]Gottardo et al. A Flexible and Powerful Bayesian Hierarchical Model for ChIP-Chip Experiments. Biometrics (2007) In press. 
\end{itemize}
Then if you use the ER data (part of it is included in this package), you should cite the following paper:
\begin{itemize}
\item[] Carroll et al 2006 \url{http://www.cell.com/content/article/abstract?uid=PIIS0092867405004538}
\end{itemize}
\part{Introduction}
	In our guide, we include example of codes that we hope will help you when using the BAC package. The codes are kept at the basic level for ease of understanding. Some of the options in the functions have been set by default. To learn more about the exact parameters and usage of each function, you may type \verb@help(FUNCTION_NAME)@ of the function of interest in R after the BAC package is loaded.
\newline

The common goal in analyzing this ChIP-chip data is to detect DNA-protein interactions from ChIP-chip experiments.
As of now, the BAC package has mainly be tested with Affymetrix tiling array data. However, we expect it to work with other platforms (e.g. Agilent, Nimblegen, cDNA, etc.). In order to use the BAC package you will need both treatment (IP) and control conditions (e.g. Mock IP) with replicates under each condition. Note that BAC does not deal with normalization, so you will have to normalize your data before hands. 
For Affymetrix arrays, we refer you to the MATR package which contains efficient normalization procedures. 


\part{Loading the BAC Package}
To load the BAC package in R, we type 
<<Reading library>>=
library(BAC)
@

\part{Detecting bound regions}
We first load the estrogen receptor data (Carroll et al. 2006).
<<Load the ER data>>=
data(ER)
@
then we calculate the (joint) posterior probabilities of enrichment based on 50 iterations for speed up, you should use more when you run the BAC function (see default parameters)
<<Calculate joint posterior probabilities>>=
# Please uncomment the following line to test the code
# BAConER<-BAC(ER[,5:7], ER[,2:4], B=50,verbose=FALSE,w=5)
# This load the resulting data obtained after executing the line above
load("bac.rda")
@
where w=5 is the window size, see parameter description for more details. Now you can have a look at these posterior probabilities to see 
where enriched regions might be, see Figure 1.
<<PProbabilities,fig=TRUE>>=
plot(ER[,1],BAConER$jointPP,pch="+",xlab="Genomic Position",ylab="Posterior probabilities")
@

Now regions can be called putative regions using the \verb@CallRegions@ function by a applying a 0.5 threshold (other thresholds can be used)

<<Call Regions>>=
ERregions<-CallRegions(ER[,1],BAConER$jointPP,cutoff=0.5,maxGap=500)
@

Finally, once we are happy with the regions detected we can easily create a BED file, which can be read and visualize in the UCSC genome browser. 

<<Create BED file>>=
# Create the BED file
nRegions<-max(ERregions)
BED<-matrix(0,nRegions,4)
for(i in 1:nRegions)
{
BED[i,2:3]<-range(ER[ERregions==i,1])
#The score should be between 0 and 1000
BED[i,4]<-max(BAConER$jointPP[ERregions==i])*1000
}
BED<-data.frame(BED)
# The ER data is a subset of chr 21
BED[,1]<-"chr21"
names(BED)<-c("chrom","chromStart","chromEnd","Score")
# print it
print(BED)
@
	

\end{document}