The following paper can also be found in the companion document in the software page.
Zhao JH, Luan JA, Tan Q, Loos R, Wareham N. Analysis of Large Genomic Data in Silico: The EPICNorfolk Study of Obesity. Huang, D.-S., Heutte, L., and Loog, M. Communication in Computer and Information System , 781-790. 2007. Springer-Verlag Berlin Heidelberg 2007
A further reference about R is as follows.
Zhao JH. Use of R in genetics associaiton studies. useR