\Header{getYeastData}{Functions to get/process yeast genome data}
\alias{findNumCol}{getYeastData}
\alias{readBadData}{getYeastData}
\keyword{manip}{getYeastData}
\begin{Description}\relax
These functions extract data from the yeast genome web site based on a
set of arguments.\end{Description}
\begin{Usage}
\begin{verbatim}
getYeastData(url, extenName, cols2Keep, sep)
readBadData(url, sep)
findNumCol(fewLines, sep)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{url}] \code{url} a character string for the url where yeast data
are stored
\item[\code{extenName}] \code{extenName} a character string for the name of
the data file of interest. The name can be a file name or with
subdirectory names under "url"
\item[\code{cols2Keep}] \code{cols2Keep} a vector of index for the columns to
be extracted from the data file
\item[\code{sep}] \code{sep} a character string for the separater used to
separate data columns in the data file
\item[\code{fewLines}] \code{fewLines} a set of character strings separated
by a new line that is going to be used to determine how many data
columns each line has
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The yeast genome web site has files stored in or in subdirectories of
\url{ftp://genome-ftp.stanford.edu/pub/yeast/data_download/} that can
be downloaded. \code{\Link{getYeastData}} extracts data from a given
file. The functions are used by an object of \code{\Link{YG-class}} to
extract data.

Some of the data in the web site may not be well fomatted (e.g. with
missing columns). \code{\Link{readBadData}} deals with these type of
data files.

\code{\Link{findNumCol}} figures out how many data columns a file
contains based on a few entries from that file.\end{Details}
\begin{Value}
\code{\Link{getYeastData}} returns a matrix containing data.

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

\code{\Link{findNumCol}} returns an integer.\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{ftp://genome-ftp.stanford.edu/pub/yeast/data_download/}\end{References}
\begin{SeeAlso}\relax
\code{\Link{YG-class}}\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
# Url may change but was correct at the time of coding
url <- "ftp://genome-ftp.stanford.edu/pub/yeast/data_download/"
temp <- getYeastData(url, "chromosomal_feature/chromosomal_feature.tab",
                         cols2Keep = c(6, 1), sep = "\t")
\end{ExampleCode}
\end{Examples}

