\Header{yeastPkgBuilder}{Functions to do a data package for yeast genome}
\alias{findYGChrLength}{yeastPkgBuilder}
\keyword{manip}{yeastPkgBuilder}
\begin{Description}\relax
These functions builds a data package for yeast genome using data from
Yeast Genome web site of Stanford University, KEGG, and Gene Ontology.\end{Description}
\begin{Usage}
\begin{verbatim}
yeastPkgBuilder(pkgName, pkgPath, base = "", srcUrls = c(KEGG =
getSrcUrl("KEGG", organism = "yeast"), GO = getSrcUrl("GO")), version =
"1.1.0", makeXML = TRUE, author = c(name = "who", address =
"who@email.com"), fromWeb = TRUE)
findYGChrLength(yGenoUrl =
"ftp://genome-ftp.stanford.edu/pub/yeast/data_download/", yGenoName =
"chromosomal_feature/chromosomal_feature.tab", toKeep = c(5, 7), sep = "\t")
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{pkgName}] \code{pkgName} a character string for the name of the
data package to be built
\item[\code{base}] \code{base} a matrix with two columns with the first one
being probe ids and the second one being their mappings to ORF (Open
Reading Frame) ids. Columns have the name "probe" and "orf"
\item[\code{pkgPath}] \code{pkgPath} a character string for the directory
where the data package to be built will be stored
\item[\code{srcUrls}] \code{srcUrls} a named vector of strings for the urls
for KEGG (\url{ftp://ftp.genome.ad.jp/pub/kegg/pathways}) and GO
(http://www.godatabase.org/dev/database/archive/2003-05-01/go\_200305-termdb.xml.gz). The urls may change over time
\item[\code{version}] \code{version} a character string for the version
number of the data package to be built
\item[\code{makeXML}] \code{makeXML} a boolean to indicate whether an XML
version of the data will be generated
\item[\code{author}] \code{author} a named vector of two character strings
with a name element for the name and an address element of email
address of the maintainer of the data package
\item[\code{fromWeb}] \code{fromWeb} a boolean to indicate whether the data
from GO should be downloaded from the web or read locally. The url
for GO should be the file name of a local file if fromWeb is
FALSE. For windows users, the data file from GO should be
downloaded/unzipped manually and set the url for GO to be the name
of the local file
\item[\code{yGenoUrl}] \code{yGenoUrl} a character string for the url to the
ftp iste where download files are stored. Defaulted to an url that
was correct at the time of writting
\item[\code{yGenoName}] \code{yGenoName} a character string for the name of
the data file that contains chromosome information
("chrosomomal\_featur/chromosomal\_feature.tab")
\item[\code{toKeep}] \code{toKeep} a vector of integers for the numbers of the
columns that will be kept when the file is read
\item[\code{sep}] \code{sep} a character of string for the delimiter used by
the file to separate columns
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Annotation elements are limited to those provided by Yeast Genome
(gene name, chromosome number, chromosomal location, GO id, and
evidence code), KEGG (path and enzyme data) and GO (GO mappings)\end{Details}
\begin{Value}
\code{findYGChrLength} returns a named vector of integers with
chromosome numbers names and length of chromosomes as values.\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.yeastgenome.org}\end{References}
\begin{Examples}
\begin{ExampleCode}
# The code runs only when invoked by an user. 
if(interactive()){
  findYGChrLength()
}
\end{ExampleCode}
\end{Examples}

