import_AllInteractions {OmnipathR} | R Documentation |
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:
import_AllInteractions( from_cache_file = NULL, filter_databases = get_interaction_databases(), select_organism = 9606 )
from_cache_file |
path to an earlier data file |
filter_databases |
interactions not reported in these databases are
removed. See |
select_organism |
Interactions are available for human, mouse and rat. Choose among: 9606 human (default), 10116 rat and 10090 Mouse |
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
A dataframe containing all the datasets in the interactions query
interactions <- import_AllInteractions(filter_databases=c("HPRD","BioGRID"), select_organism = 9606)