\HeaderA{pdnn.params.chiptype}{A function to fit PDNN parameters}{pdnn.params.chiptype}
\keyword{manip}{pdnn.params.chiptype}
\begin{Description}\relax
A function to fit PDNN parameters that are chip-type specific
\end{Description}
\begin{Usage}
\begin{verbatim}
pdnn.params.chiptype(energy.param.file, probes.file = NULL, probes.pack= NULL,
                     probes.data.frame = NULL,
                     seq.name, x.name, y.name, affyid.name, verbose = TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{energy.param.file}] Path to the energy data file (see details) 
\item[\code{probes.file}] Path to the probe files (see details) 
\item[\code{probes.pack}] Name of the probe pack (see details) 
\item[\code{probes.data.frame}] A \code{data.frame}
\item[\code{seq.name, x.name, y.name, affyid.name}] The names of the columns
in the data.frame from \code{probes.pack} or \code{probes.file} for
the probe sequences, the X positions, the Y positions and the probe
set ID respectively
\item[\code{verbose}] verbosity (\code{TRUE} or \code{FALSE}) 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The parameters \code{probes.file}, \code{probes.pack} and
\code{probes.data.frame} are mutually exclusive.
The function fits PDNN parameters that are specific to chip-types
(hence specific to the probe sequences).
It requires data files like the one found on Li Zhang's web page:
(http://odin.mdacc.tmc.edu/~zhangli/PerfectMatch/)
This should be computed once for all for a given chip type.
Computed values for the chips are included in the package.
This allows 'automagic' use of them when these chips types are used
(as done in the function \code{\LinkA{expressopdnn}{expressopdnn}}).
\end{Details}
\begin{Value}
A list of:
\begin{ldescription}
\item[\code{Eg}] environment. One entry per dinucleotide.
\item[\code{Wg}] numerical vector
\item[\code{En}] environment. One entry per dinucleotide.
\item[\code{Wn}] numerical vector
\item[\code{params.gene}] environment. One entry per gene, each entry is
is a list of elements Sg, Sn, xy  and gene.i
\end{ldescription}
\end{Value}
\begin{Section}{warning}
The X and Y positions in the \code{data.frame} are expected to be
original ones in the Affymetrix files (starting at zero. They are offset by one within
this function.
\end{Section}
\begin{SeeAlso}\relax
\code{\LinkA{find.params.pdnn}{find.params.pdnn}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
if (interactive()) {
  energy.file <- system.file("exampleData", "pdnn-energy-parameter_hg-u95av2.txt", package="affypdnn")

  params.chiptype <- pdnn.params.chiptype(energy.file, probes.pack="hgu95av2probe")
}

\end{ExampleCode}
\end{Examples}

