OmnipathR {OmnipathR} | R Documentation |
OmnipathR is an R package built to provide easy access to the data stored in the Omnipath webservice:
The webservice implements a very simple REST style API. This package make requests by the HTTP protocol to retreive the data. Hence, fast Internet access is required for a propser use of OmnipathR.
The package also provides some utility functions to filter, analyse and visualize the data.
Alberto Valdeolivas <alvaldeolivas@gmail> and Attila Gabor <gaborattila87@gmail.com>
# Download post-translational modifications: ptms = import_Omnipath_PTMS(filter_databases=c("PhosphoSite", "Signor")) # Download protein-protein interactions interactions = import_Omnipath_Interactions(filter_databases=c("SignaLink3")) # Convert to igraph objects: ptms_g = ptms_graph(ptms = ptms ) OPI_g = interaction_graph(interactions = interactions ) # Print some interactions: print_interactions(head(ptms)) # interactions with references: print_interactions(tail(ptms),writeRefs=TRUE) # find interactions between kinase and substrate: print_interactions(dplyr::filter(ptms,enzyme_genesymbol=="MAP2K1", substrate_genesymbol=="MAPK3")) # find shortest paths on the directed network between proteins printPath_es(shortest_paths(OPI_g,from = "TYRO3",to = "STAT3", output = 'epath')$epath[[1]],OPI_g) # find all shortest paths between proteins printPath_vs(all_shortest_paths(ptms_g,from = "SRC",to = "STAT1")$res,ptms_g)