import_AllInteractions {OmnipathR}R Documentation

Imports from Omnipath webservice all the available interactions from the different datasets

Description

Imports the dataset from: http://omnipathdb.org/interactions?datasets=omnipath,pathwayextra,kinaseextra,ligrecextra,tfregulons,mirnatarget&fields=sources,references&genesymbols=1, which contains all the different interactions available in the webserver:

Usage

import_AllInteractions(
  from_cache_file = NULL,
  filter_databases = get_interaction_databases(),
  select_organism = 9606
)

Arguments

from_cache_file

path to an earlier data file

filter_databases

interactions not reported in these databases are removed. See get_interaction_databases for more information.

select_organism

Interactions are available for human, mouse and rat. Choose among: 9606 human (default), 10116 rat and 10090 Mouse

Details

omnipath: the OmniPath data as defined in the paper, an arbitrary optimum between coverage and quality pathwayextra: activity flow interactions without literature reference kinaseextra: enzyme-substrate interactions without literature reference ligrecextra: ligand-receptor interactions without literature reference tfregulons: transcription factor (TF)-target interactions from DoRothEA mirnatarget: miRNA-mRNA and TF-miRNA interactions

Value

A dataframe containing all the datasets in the interactions query

See Also

get_interaction_databases

Examples

interactions <- import_AllInteractions(filter_databases=c("HPRD","BioGRID"),
    select_organism = 9606)

[Package OmnipathR version 1.0.1 Index]