I need to do epistasis analysis between two sets of SNPs (each contains ~1000 SNPs). I am interested in pairwise interactions between the SNPs on different sets and not between SNPs on same set. I am aware of the epistasis option in Plink and I have used that. I just need to know if there is any other software that does it, so that I can validate my findings. I tried searching for R packages. Most of the available R packages does analysis on a single set of SNPs with all possible pairwise combinations and none (at least to my knowledge) takes up two separate sets of SNPs. Is there any software (or possible a R package) that does this? Thanks
Dear Veera,
Please find attached the recent paper of Li et al. (2014): "A FAST ALGORITHM FOR DETECTING GENE–GENE INTERACTIONS IN GENOME-WIDE ASSOCIATION STUDIES".
It will surely help you.
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