\Header{UG-class}{Class "UG" a sub-class of pubRepo to handle data from UniGene}
\alias{organism}{UG-class}
\alias{organism<\Rdash}{UG-class}
\alias{UG}{UG-class}
\keyword{classes}{UG-class}
\begin{Description}\relax
This class is a sub-class of pubRepo that is implemented
specifically to parse data from UniGene (XX.data.gz, where XX is a
abbreviation for a given organism)\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("UG", ...)}.
A constructor (UG) is available and should be used to instatiate
objects of this class\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{organism}:] Object of class \code{"character"} a
character string for the name of the organism of concern
\item[\code{srcUrl}:] Object of class \code{"character", from class
        "pubRepo"} a character string for the url of the source data
\item[\code{parser}:] Object of class \code{"character", from class
        "pubRepo"}  a character string for the name of the file
containing a segment of perl code with instructions on how the
source data will be processed and output be generated 
\item[\code{baseFile}:] Object of class \code{"character", from
        class "pubRepo"} a character string for the name of the file
that contains data that will be used as the base to process the
source data.  Data from the source that are related to elements in
the base file will be extracted. baseFile is assumed to be a two
folumn file with the first column being some type of arbitrary ids
(e.g. Affymetrix probe ids) and the second cloumn being the
corresponding ids of a given public repository (e.g. GenBank
accession numbers or UniGene ids)
}\end{Section}
\begin{Section}{Extends}
Class \code{"pubRepo"}, directly.\end{Section}
\begin{Section}{Methods}
\describe{
\item[organism<-] \code{signature(object = "UG")}: Sets the value
for the organism slot
\item[organism] \code{signature(object = "UG")}: Gets the value for
the organism slot
}\end{Section}
\begin{Note}\relax
This class is part of 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{www.ncbi.nlm.nih.gov/UniGene}\end{References}
\begin{SeeAlso}\relax
\code{\Link{pubRepo-class}}\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
if(interactive()){
# Parse a truncated version of Hs.data.gz from Bioconductor
path <- file.path(.path.package("pubRepo"), "data")
temp <- matrix(c("32469_f_at", "D90278", "32469_at", "L00693", "33825_at",
"X68733", "35730_at", "X03350", "38912_at", "D90042", "38936_at",
"M16652"), ncol = 2, byrow = TRUE)
write.table(temp, "tempfile", sep = "\t", quote = FALSE,
row.names = FALSE, col.names = FALSE)  
ug <- UG(srcUrl =
"http://www.bioconductor.org/datafiles/wwwsources/Ths.data.gz",
parser = file.path(path, "basedUGParser"), baseFile = "tempfile",
organism = "human")
data <- parseData(ug)
unlink("tempfile")
}
\end{ExampleCode}
\end{Examples}

