%\VignetteIndexEntry{keggorth overview}
%\VignetteDepends{hgu95av2.db, graph, RBGL, ALL}
%\VignetteKeywords{Annotation, Pathways}
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\begin{document}
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\title{\Rpackage{keggorth}: the KEGG orthology as \Robject{graph}}
\author{VJ Carey}% \verb+<stvjc@channing.harvard.edu>+}
\maketitle
\tableofcontents

\section{Introduction}

KEGG is the Kyoto Encyclopedia of Genes and Genomes.
An important product of the KEGG group is a catalog
of pathways.  The KEGG Orthology (KO)
organizes the pathways into a conceptual hierarchy.
This package encodes the hierarchy as a graph, and
provides some support for deriving sets of array
feature identifiers from the hierarchy.

\section{\Robject{KOgraph}}

<<lkkog>>=
library(keggorth)
data(KOgraph)
KOgraph
nodes(KOgraph)[1:5]
@
The upper component of the hierarchy is:
<<lkr>>=
adj(KOgraph, nodes(KOgraph)[1])
@

Graph operations can be used to explore the
orthology.  For example, the context of
the PPAR signaling pathway is found
as follows:
<<lkpa>>=
library(RBGL)
sp.between(KOgraph, nodes(KOgraph)[1], "PPAR signaling pathway")
@

Fixed-length identifiers are used to label pathways.
These are available as the 'tag' nodeData attribute.
<<lkta>>=
nodeData(KOgraph,,"tag")[1:5]
@
The depth of each term is also available.
<<lkde>>=
nodeData(KOgraph,,"depth")[1:5]
@

\section{Application to gene filtering}

Several functions are available for retrieving
relevant information from the orthology.
If you know a substring of the pathway name of interest,
you can obtain the numerical tag(s).
<<lkd>>=
getKOtags("insulin")
@

We can get probe set identifiers corresponding to
a term.  The default chip annotation package used is hgu95av2.db.
<<lkp>>=
library(hgu95av2.db)
mp = getKOprobes("Methionine")
library(ALL)
data(ALL)
ALL[mp,]
@

\section{Infrastructure considerations}

The graph was built through manual massaging of
an HTML page in which the orthology was expanded
to level 3.  This operation needs to be programmatic,
and the version number needs to be made clear.

The HTML source from which this was built is in inst/keggHTML
in the source package.

\section{Session info}

<<lksi>>=
sessionInfo()
@


\end{document}