\Header{getChroLocation}{Functions to extract data from golden path}
\alias{getGPData}{getChroLocation}
\alias{gpLinkNGene}{getChroLocation}
\keyword{manip}{getChroLocation}
\begin{Description}\relax
These functions are used by objects GP to extract chromosomal location
and orientation data for genes.\end{Description}
\begin{Usage}
\begin{verbatim}
getChroLocation(srcUrl, exten = gpLinkNGene(), sep = "\t", fromWeb = TRUE)
getGPData(srcUrl, sep = "\t", ncol = 8, keep = c(3,7))
gpLinkNGene(test = FALSE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{srcUrl}] \code{srcUrl} a character string for the url where
source data are available
\item[\code{exten}] \code{exten} a character string for the name of the file
to be used for the extraction
\item[\code{sep}] \code{sep} a character string for the separater used by the
source file
\item[\code{ncol}] \code{ncol} an integer for the total number of columns a
source data set has
\item[\code{keep}] \code{keep} a numeric vector for the columns (defined by
column number) to be kept
\item[\code{test}] \code{test} a boolean to indicate whether the process is
in a testing mode
\item[\code{fromWeb}] \code{fromWeb} a boolean to indicate whether the source
data should be downloaded from the web or is a local file
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\code{\Link{getChroLocation}} extracts chromosomal location data from
a data file named refGene.

\code{\Link{getGPData}} Reads data from a source data file defined by
srcUrl and returns them as a matrix.

\code{\Link{gpLinkNGene}} returns a correct link and gene data file
names that will be used to get chromosomal location data.\end{Details}
\begin{Value}
\code{\Link{getChroLocation}} returns a matrix with the first column
being LocusLink ids, the second being the chromosomal location, and
third being the orientation for that locus.

\code{\Link{getGPData}} returns a matrix.

\code{\Link{gpLinkNGene}} returns a named vector.\end{Value}
\begin{Note}\relax
The functions are part of the Bioconductor project at Dana-Farber
Cancer Institute to provide Bioinformatics functionalities through R\end{Note}
\begin{Author}\relax
Jianhua Zhang\end{Author}
\begin{References}\relax
\url{http://www.genome.ucsc.edu}\end{References}
\begin{SeeAlso}\relax
\code{\Link{GP}}\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# Truncated versions of files stored in Bioconductor site are used
gpLinkNGene(test = FALSE)
temp <- getGPData(
"http://www.bioconductor.org/datafiles/wwwsources/Tlink.txt",
sep = "\t", ncol = 8, keep = c(3,7))
temp <- getChroLocation(
"http://www.bioconductor.org/datafiles/wwwsources/",
exten = gpLinkNGene(TRUE), sep = "\t")
\end{ExampleCode}
\end{Examples}

