The OmnipathR package

Description

OmnipathR is an R package built to provide easy access to the data stored in the Omnipath webservice:

http://omnipathdb.org/

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.

Author(s)

Alberto Valdeolivas <alvaldeolivas@gmail> and Attila Gabor <gaborattila87@gmail.com>

Examples

# 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)