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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,
  ...
)

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.

...

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
)