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\title{readMAPPER: Interface to MAPPER TFBS database}
\author{Alberto Riva and Heike Sichtig (U. of Florida) }

\maketitle

% for cutting and pasting use continue =""
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<<setup, echo=FALSE>>=
library(RMAPPER)
options(warn=-1, width=75, digits=2, scipen=3,  "prompt" = "R> ", "continue" = " ")
@

\section{Introduction}
The \pkg{RMAPPER} package provides an interface to the MAPPER database
of predicted Transcription Factor Binding Sites (TFBS). The 
MAPPER database (\url{http://genome.ufl.edu/mapper/}) contains predicted 
binding sites for over 800 Transcription Factors in the promoter 
regions of all human, mouse and Drosophila genes. This package 
allows you to query the database according to the desired 
parameters and to download the resulting set of TFBS into an R object.

\section{readMAPPER demonstration}
First, the user should load the RMAPPER library.

<<install, eval=FALSE, keep.source=TRUE>>=
 library(RMAPPER)
@

Then, examples can be run using the example function or directly using \emph{readMAPPER}.
The functions \Rcmd{query} and\Rcmd{hits} are available to display the exact query and 
details of hits respectively.
Note that the value for the "models" parameter should be a comma-separated
list of model accession numbers. A table listing all transcription
factors known to MAPPER with the corresponding model accession
numbers is available at: \url{http://genome.ufl.edu/mapper/factors-table}.
It can also be retrieved in R by evaluating:
<<factortable, eval=FALSE>>=
 rmapperFactorTable("*")
@
Use the following R command to get the model accession numbers known to 
MAPPER for a specific transcription factor, i.e. "AbaA".
<<AbaA, eval=FALSE>>=
 rmapperFactorTable("AbaA")
@
Use the following R command to get the model accession numbers known to 
MAPPER for all transcription factors starting with "Ab...".
<<Ab, eval=FALSE>>=
 rmapperFactorTable("Ab")
@

\subsection{Example 1}
Retrieve predicted hits for model "MOOO27" (abaA) in 
the promoter of transcript NM\_009696 (mouse Apoe). Only 
hits with a score above the 95th percentile will be returned. 
<<example1>>=
 mh = readMAPPER(gene="NM_009696", perc="95", models="M00027")
 mh
 query(mh)
 hits(mh)
@

\subsection{Example 2}
Retrieve predicted hits for models "MOOO27" (abaA) and
"M00442" (ABF) in the promoter of transcript NM\_009696
(mouse Apoe). Only hits with a score greater than 3 will 
be returned.
<<example2>>=
  mh = readMAPPER(gene="NM_009696", score="3", models="M00027,M00442")
  mh
  query(mh)
  hits(mh)
@

\section{Help}
You can issue the following R command for help. 
<<help, eval=FALSE>>=
 rmapperHelp()
@

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