* added a novel pathway analysis method based on the primary dis-regulation of the genes in each pathway


* add the ability to analyze gene sets (pathways with no interaction) using only over-representation
* bug fixes: plot boundaries, etc.


Initial release of package ROntoTools includes:

* pe: Pathway analysis tool Pathway-Express with the following features:
    - perform pathway analysis on pathways defined in the standard graph format
provided by the package graph
    - perform the analysis using either differentially expressed (DE) genes or
using a cut-of-free analysis
    - when available, use both information related to the strangth of the inter-
action between the genes (as edgeWeights) and the relevance of each gene (as 
    - the results are summerized using the generic function Summary

* keggPathwayGraphs/keggPathwayNames: Utility to download and parse the KEGG 
pathways data in graph objects:
    - based on the work in the packages KEGGREST and KEGGgraph

* nodeWeigths: the missing generic convenience function from package graph to 
get the node weights of a graph

* alpha1MR/alphaMLG: two utilites to transform the a vector of p-values into 
weights to be used as nodeWeights