\HeaderA{chromLocation-class}{Class chromLocation, a class for describing genes and their
chromosome mappings.}{chromLocation.Rdash.class}
\aliasA{chromInfo}{chromLocation-class}{chromInfo}
\aliasA{chromInfo,chromLocation-method}{chromLocation-class}{chromInfo,chromLocation.Rdash.method}
\aliasA{chromLengths}{chromLocation-class}{chromLengths}
\aliasA{chromLengths,chromLocation-method}{chromLocation-class}{chromLengths,chromLocation.Rdash.method}
\aliasA{chromLocs}{chromLocation-class}{chromLocs}
\aliasA{chromLocs,chromLocation-method}{chromLocation-class}{chromLocs,chromLocation.Rdash.method}
\aliasA{chromNames}{chromLocation-class}{chromNames}
\aliasA{chromNames,chromLocation-method}{chromLocation-class}{chromNames,chromLocation.Rdash.method}
\aliasA{dataSource}{chromLocation-class}{dataSource}
\aliasA{dataSource,chromLocation-method}{chromLocation-class}{dataSource,chromLocation.Rdash.method}
\aliasA{geneSymbols}{chromLocation-class}{geneSymbols}
\aliasA{geneSymbols,chromLocation-method}{chromLocation-class}{geneSymbols,chromLocation.Rdash.method}
\aliasA{nChrom}{chromLocation-class}{nChrom}
\aliasA{nChrom,chromLocation-method}{chromLocation-class}{nChrom,chromLocation.Rdash.method}
\aliasA{organism}{chromLocation-class}{organism}
\aliasA{organism,chromLocation-method}{chromLocation-class}{organism,chromLocation.Rdash.method}
\aliasA{probesToChrom}{chromLocation-class}{probesToChrom}
\aliasA{probesToChrom,chromLocation-method}{chromLocation-class}{probesToChrom,chromLocation.Rdash.method}
\aliasA{show,chromLocation-method}{chromLocation-class}{show,chromLocation.Rdash.method}
\keyword{classes}{chromLocation-class}
\begin{Description}\relax
This class provides chromosomal information provided by a
Bioconductor metadata package.  By creating the object once for a
particular package, it can be used in a variety of locations without
the need to recomputed values repeatedly.
\end{Description}
\begin{Section}{Creating Objects}
\code{  new('chromLocation',}\\
\code{    organism     = ...., \# Object of class character}\\
\code{    dataSource    = ...., \# Object of class character}\\
\code{    chromLocs    = ...., \# Object of class list}\\
\code{    probesToChrom  = ...., \# Object of class environment}\\
\code{    chromInfo    = ...., \# Object of class numeric}\\
\code{    geneSymbols  = ...., \# Object of class environment}\\
\code{  )}
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{organism}:] Object of class "character".  The organism
that these genes correspond to. 
\item[\code{dataSource}:] Object of class "character".  The source of
the gene data. 
\item[\code{chromLocs}:] Object of class "list".  A list which
provides specific location information for every gene. 
\item[\code{probesToChrom}:] Object of class "genEnv".  A hash table
which will translate a probe identifier to chromosome it belongs to. 
\item[\code{chromInfo}:] A numerical vector representing each
chromosome, where the names are the names of the chromosomes and
the values are their lengths
\item[\code{geneSymbols}:] An environment that maps a probe ID to
the appropriate gene symbol
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[chromLengths] (chromLocation): Gets the lengths of the
chromosome for this organism
\item[chromLocs] (chromLocation): Gets the 'chromLocs' attribute. 
\item[chromNames] (chromLocation): Gets the name of the chromosomes
for this organism
\item[dataSource] (chromLocation): Gets the 'dataSource' attribute. 
\item[probesToChrom] (chromLocation): Gets the 'probesToChrom' attribute. 
\item[nChrom] (chromLocation): gets the number of chromosomes this
organism has
\item[organism] (chromLocation): gets the 'organism' attribute. 
\item[chromInfo] Gets the 'chromInfo' attribute. 
\item[geneSymbols] Gets the 'geneSymbols' attribute. 
}
\end{Section}
\begin{SeeAlso}\relax
\code{\LinkA{buildChromLocation}{buildChromLocation}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
   curWarn <- getOption("warn")
   options(warn=0)
   on.exit(options(warn=curWarn), add=TRUE)
   if (require("hgu95av2")) {
     z <- buildChromLocation("hgu95av2")

     ## find the number of chromosomes
     nChrom(z)

     ## Find the names of the chromosomes
     chromNames(z)

     ## get the organism this object refers to
     organism(z)

     ## get the lengths of the chromosomes in this object
     chromLengths(z)

   } else print("This example requires the hgu95av2 data package")
\end{ExampleCode}
\end{Examples}

