EBEN-epistasis is a pipeline on analyzing the main and epistasis effect of genetic and epigenetic factors, in company with the following manuscript.
J Wen, A Quitadamo, B Hall and X Shi. An Empirical Bayesian Elastic Nets Method for Epistasis Analysis of microRNAs on Pathological Stages in Colon Cancer. BMC Genomics. In press.
The R package EBEN_4.6.tgz can be found in https://cran.r-project.org/web/packages/EBEN/index.html. The more details on EBNE algorithm can be reached in Huang A., Xu S., Cai X. EBEN for multiple QTL mapping. Heredity. (2014) 10.1038/hdy.2014.79.
The bc_matrix.txt includes the miRNA expression data and the pathological data.
The R script EBEN-epistasis.R shows the whole pipeline to analyze the main and epistasis effect of microRNA expression on pathological stages of colon cancer. This pipeline can be adjusted to investigate the main and epistasis effect of other biological entities using appropriate datasets.