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The interaction datasets currently available in OmniPath:

Usage

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

import_AllInteractions(...)

Arguments

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

Character: datasets or resources 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.

strict_evidences

Logical: restrict the evidences to the queried datasets and resources. If set to FALSE, the directions and effect signs and references might be based on other datasets and resources.

...

Passed to import_all_interactions.

Value

A dataframe containing all the datasets in the interactions query

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

Examples

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