All post-translational interactions from OmniPath

Imports interactions from all post-translational datasets of OmniPath. The datasets are "omnipath", "kinaseextra", "pathwayextra" and "ligrecextra".

Usage

import_post_translational_interactions(
  resources = NULL,
  organism = 9606,
  exclude = NULL,
  references_by_resource = TRUE,
  strict_evidences = FALSE,
  ...
)

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

exclude

Character: datasets or resources to exclude.

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.

...

optional additional arguments

Value

A dataframe containing post-translational interactions

See also

• get_interaction_resources

• import_all_interactions

• interaction_graph

• print_interactions

Examples

interactions <-
    import_post_translational_interactions(
        resources = c('BioGRID')
    )