\HeaderA{readClfEnv}{Parsing a CLF file using Affymetrix Fusion SDK}{readClfEnv}
\keyword{file}{readClfEnv}
\keyword{IO}{readClfEnv}
\begin{Description}\relax
This function parses a CLF file using the Affymetrix Fusion SDK. CLF
(chip layout) files contain information associating probe ids with chip
x- and y- coordinates.
\end{Description}
\begin{Usage}
\begin{verbatim}
readClfEnv(file, readBody = TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{file}] \code{character(1)} providing a path to the CLF file to be
input.
\item[\code{readBody}] \code{logical(1)} indicating whether the entire file should
be parsed (\code{TRUE}) or only the file header information describing
the chips to which the file is releavant.
\end{ldescription}
\end{Arguments}
\begin{Value}
An enviroment. The \code{header} element is always present; the
remainder are present when \code{readBody=TRUE}.
\begin{ldescription}
\item[\code{header}] A list with information about the CLF file. The list
contains elements described in the CLF file format document
referenced below.
\item[\code{dims}] A length-two integer vector of chip x- and y-coordinates.
\item[\code{id}] An integer vector of length \code{prod(dims)} containing
probe identifiers.
\item[\code{x}] An integer vector of length \code{prod(dims)} containing
x-coordinates corresponding to the entries in \code{id}.
\item[\code{y}] An integer vector of length \code{prod(dims)} containing
y-coordinates corresponding to the entries in \code{id}.
\end{ldescription}
\end{Value}
\begin{Author}\relax
Martin Morgan \url{mtmorgan@fhcrc.org}
\end{Author}
\begin{SeeAlso}\relax
\url{https://www.affymetrix.com/support/developer/fusion/File_Format_CLF_aptv161.pdf}
describes CLF file content.
\end{SeeAlso}

