I would like to do a genome wide gene x environment interaction analysis in a matched (1-1) case control samples. I referred all related previous publications and in most of the papers authors used either STATA or SAS for targeted variants analysis and none found for a genome wide scale. I got few references for performing conditional logisitic regression in R, for example using survival (clogit) package. But I couldn't find any reference for adding interaction terms in conditional logistic models in R. Can someone help me with references for interaction analysis using conditional logistic regression in R or any similar program ?