OmnipathR: The OmnipathR package

In OmnipathR: OmniPath web service client

Description

OmnipathR is an R package built to provide easy access to the data stored in the OmniPath web service:

https://omnipathdb.org/

The web service 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 Denes Turei <[e-mail]> and Attila Gabor <[e-mail]>

Examples

# Download post-translational modifications:
ptms = import_omnipath_enzsub(resources=c("PhosphoSite", "SIGNOR"))

# Download protein-protein interactions
interactions = import_omnipath_interactions(resources=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
print_path_es(shortest_paths(OPI_g,from = "TYRO3",to = "STAT3",
   output = 'epath')$epath[[1]],OPI_g)

# find all shortest paths between proteins
print_path_vs(
    all_shortest_paths(
        ptms_g,
        from = "SRC",
        to = "STAT1"
    )$res,
    ptms_g
)

OmnipathR documentation built on Nov. 8, 2020, 8:10 p.m.