Does anyone happen to know what source / processing was used to construct the "gerstein-2012" annotations in the RefNet package?
It appears that the network includes 6896 edges:
library('RefNet') refnet = RefNet() ixns = interactions(refnet, species="9606", provider=c("gerstein-2012")) nrow(ixns) # 6895
I would have suspected that the data used to construct the annotations would have come from http://encodenets.gersteinlab.org/, but none of the correpsonding files there are of a similar size:
wc -l * 26070 enets2.Proximal_filtered.txt 19258 enets3.Distal.txt
Is there another source that I've missed? Or was some additional processing down on the dataset resulting in a subset of the original edges?