import_all_interactions: Imports all interaction datasets available in OmniPath

In OmnipathR: OmniPath web service client

Description

The interaction datasets currently available in OmniPath:

Usage

import_all_interactions(
  cache_file = NULL,
  resources = NULL,
  organism = 9606,
  dorothea_levels = c("A", "B"),
  exclude = NULL,
  fields = NULL,
  default_fields = TRUE,
  references_by_resource = TRUE,
  ...
)

import_AllInteractions(...)

Arguments

cache_file	path to an earlier data file
resources	interactions not reported in these databases are removed. See get_interaction_resources for more information.
organism	Interactions are available for human, mouse and rat. Choose among: 9606 human (default), 10116 rat and 10090 Mouse
dorothea_levels	The confidence levels of the dorothea interactions (TF-target) which range from A to D. Set to A and B by default.
exclude	datasets to exclude
fields	The user can define here the fields to be added. If used, set the next argument, 'default_fields', to FALSE.
default_fields	whether to include the default fields (columns) for the query type. If FALSE, only the fields defined by the user in the 'fields' argument will be added.
references_by_resource	if FALSE, removes the resource name prefixes from the references (PubMed IDs); this way the information which reference comes from which resource will be lost and the PubMed IDs will be unique.
...	Passed to import_all_interactions.

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 dorothea: transcription factor (TF)-target interactions from DoRothEA tf_target: transcription factor (TF)-target interactions from other resources mirnatarget: miRNA-mRNA interactions tf_mirna: TF-miRNA interactions lncrna_mrna: lncRNA-mRNA interactions

Value

A dataframe containing all the datasets in the interactions query

See Also

get_interaction_resources

Examples

interactions <- import_all_interactions(
    resources = c('HPRD', 'BioGRID'),
    organism = 9606
)

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