OmnipathR {OmnipathR} | R Documentation

## The OmnipathR package

### 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 <turei.denes@gmail.com> and Attila Gabor <gaborattila87@gmail.com>

### 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
    )

[Package OmnipathR version 2.0.0 Index]