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\author{Jeff Gentry}

\begin{document}
\title{HowTo: Build and use chromosomal information}
\maketitle{}

\section{Overview}

The annotate package provides a class that can be used to model
chromosomal information about a species, using one of the metadata
packages provided by Bioconductor.  This class contains information
about the organism and its chromosomes and provides a standardized
interface to the information in the metadata packages for other
software to quickly extract necessary chromosomal information.  An
example of using \Rclass{chromLocation} objects in other software can
be found with the \Rfunction{alongChrom} function of the
\Rpackage{geneplotter} package in Bioconductor.

\section{The chromLocation class}

The \Rclass{chromLocation} class is used to provide a structure for
chromosomal data of a particular organism.  In this section, we will
discuss the various slots of the class and the methods for interacting
with them.  Before this though, we will create an object of class
\Rclass{chromLocation} for demonstration purposes later.  The helper
function \Rfunction{buildChromLocation} is used, and it takes as an
argument the name of a Bioconductor metadata package, which is itself
used to extract the data.  For this vignette, we will be using the
\Rpackage{hgu95av2} package.

<<buildCL>>=
library("annotate")
z <- buildChromLocation("hgu95av2")
z
@

Once we have an object of the \Rclass{chromLocation} class, we can now
access its various slots to get the information contained within it.
There are six slots in this class:
\begin{verbatim}
organism:       This lists the organism that this object is describing.
dataSource:     Where this data was acquired from.
chromLocs:      A list with an element for every unique chromosome 
                name, where each element contains a named vector where
                the names are probe IDs and the values describe the
                location of that probe on the chromosome.  Negative
                values indicate that the location is on the antisense
                strand. 
probesToChrom:  A hash table which will translate a probe ID to the 
                chromosome it belongs to.
chromInfo:      A numerical vector representing each chromosome, where
                the names are the names of the chromosomes and the
                values are the lengths of those chromosomes.
geneSymbols:    An environment that maps a probe ID to the appropriate
                gene symbol.
\end{verbatim}

There is a basic 'get' type method for each of these slots, all with
the same name as the respective slot.  In the following example, we
will demonstrate these basic methods.  For the
\Rfunction{probesToChrom} and \Rfunction{geneSymbols} methods, the
return value is an environment which maps a probe ID to other values,
we will be using the probe ID '32972\_at', which was selected at
random for these examples.  We are showing only part of the
\Rfunction{chromLocs} method's output as it is quite long in its entirety.

<<showBasicMethods>>=
organism(z)

dataSource(z)

## The chromLocs list is extremely large.  Let's only
## look at one of the elements.
names(chromLocs(z))
chromLocs(z)[["Y"]]

get("32972_at", probesToChrom(z))

chromInfo(z)

get("32972_at", geneSymbols(z))

@

Another method which can be used to access information about the
particular \Rclass{chromLocation} object is the \Rfunction{nChrom}
method, which will list how many chromosomes this organism has:

<<nChrom>>=
nChrom(z)
@

\section{Summary}

The \Rclass{chromLocation} class has a simple design, but can be
powerful if one wants to store the chromosomal data contained in a
Bioconductor package into a single object.  These objects can be
created once and then passed around to multiple functions, which can
cut down on computation time to access the desired information from
the package.  These objects allow access to basic but also important
information, and provide a standard interface for writers of other
software to access this information.

\end{document}
