\Header{chromLocation-class}{Class chromLocation, a class for describing genes and their
chromosome mappings.}
\alias{chromInfo}{chromLocation-class}
\alias{chromLengths}{chromLocation-class}
\alias{chromLocs}{chromLocation-class}
\alias{chromNames}{chromLocation-class}
\alias{dataSource}{chromLocation-class}
\alias{geneSymbols}{chromLocation-class}
\alias{nChrom}{chromLocation-class}
\alias{organism}{chromLocation-class}
\alias{probesToChrom}{chromLocation-class}
\keyword{classes}{chromLocation-class}
\begin{Description}\relax
This class provides a mechanism for mapping a set of
genes to their respective locations in chromosomes.
Details on how to construct an object of this class from Bioconductor
data packags are given in the \code{byChroms} vignette in the
\code{geneplotter} package.\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}

