Readme

The package is build on top of topGO package. 
topGO is a bioconductor package written by by Alexa. It's designed specifically for Gene ontology enrichment analysis.
topOnto is a generalized version of topGO where any GO-like ontology can be used.

topOnto loads ontology from topOnto.xxx.db packages.
You can create your own topOnto.xxx.db packages with your ontology obo file by following the instruction in inst/scripts/create.db

For illustration purpose, the topOnto.HDO.db is pre-created in inst/scripts/create.db/topOnto.HDO.db.
If you want to run the example for topOnto, the topOnto.HDO.db package will be installed druing the installation process.

Here's what you need to do to install topOnto
cd to the package root folder
	$cd xx/topOnto/
run the install.sh to build the packages from source:
	$sh install.sh


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***inst/scripts/exampleRun.R. is a small example to get you start.
***You need to load an Annotation file for the ontology you choose and a geneList of interests.
***You can then change the file path in the script to your own annotation file and gene list.
***In the exmaple, we used human_g2d_omim.txt as the gene annotation file.
***For more analysis method with topOnto, please ref to here: http://www.bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf
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