Hello,
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?
Keith
Hi Paul,
Thanks for the response and clarification. I think that the dataset you are using is actually from an earlier paper out of the Gerstein lab -- "Rewiring of Transcriptional Regulatory Networks: Hierarchy, Rather Than Connectivity, Better Reflects the Importance of Regulators" (2010).
The datasets associated with the ENCODE paper are on http://encodenets.gersteinlab.org/.
I could see both being useful for some people, so it probably wouldn't hurt to include both the datasets. It might also be worth it to include the source of each of the datasets in the documentation. To be even more explicit, you could even include the scripts you used to generate each of the external RData-based providers.
Thanks for your work putting this useful package together!
All the best,
Keith