\HeaderA{chkMotif4TF}{analyze relationship between motif frequency
and binding intensity for selected motif and TF}{chkMotif4TF}
\aliasA{chkAllUS}{chkMotif4TF}{chkAllUS}
\keyword{models}{chkMotif4TF}
\begin{Description}\relax
analyze relationship between motif frequency
and binding intensity for selected motif and TF
\end{Description}
\begin{Usage}
\begin{verbatim}
chkMotif4TF(motif, TF, chset, upstr, bthresh=2, countthresh=0)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{motif}] character string in alphabet known to Biostrings
\item[\code{TF}] name of a TF (sample name in the ChIP-chip data
structure \code{chset}
\item[\code{chset}] an ExpressionSet instance harboring ChIP-chip data

\item[\code{upstr}] an instance of upstreamSeqs
\item[\code{bthresh}] threshold for binding intensity results to
declare TF 'bound' to the upstream region
\item[\code{countthresh}] threshold for motif count to be considered
'present' in upstream region
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Uses \code{\LinkA{countPattern}{countPattern}} to perform 
motif count.
\end{Details}
\begin{Value}
a list with elements \code{call}, \code{table},
and \code{test}, the latter providing the result of
\code{\LinkA{fisher.test}{fisher.test}}
\end{Value}
\begin{Author}\relax
Vince Carey <stvjc@channing.harvard.edu>
\end{Author}
\begin{Examples}
\begin{ExampleCode}
# slow
## Not run: 
data(harbChIP)
data(sceUpstr)
chkMotif4TF("CGGCCG", "RDS1", harbChIP, sceUpstr)
## End(Not run)
\end{ExampleCode}
\end{Examples}

