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The function of STAMS_reademe file is teaching us to construct the mapped_data? I suppose that a detailed describtion of input_file would be very helpful. I have obtained the results from VEGAS, but not sure how to use it in the STAMS. Hope to your reply.

I recommend using the STRINGdb R package to map the output of VEGAS to STRING identifiers. There are a lot of ways to map gene names to STRING ids, and they have a very comprehensive treatment of the problem.