For anyone working with iRefR (the R package for iRefIndex) you may be interested in a recent paper that includes R code using iRefR for all Figures in the paper.
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction
BMC Bioinformatics.2012, 13:294.
URL: http://www.biomedcentral.com/1471-2105/13/294
Best regards
Ian