import_all_interactions: Imports all interaction datasets available in OmniPath

In saezlab/OmnipathR: OmniPath web service client and more

Imports all interaction datasets available in OmniPath

Description

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,
  genesymbol_resource = NULL,
  types = NULL,
  ...
)

import_AllInteractions(...)

Arguments

resources	interactions not reported in these databases are removed. See get_interaction_resources for more information.
organism	Character or integer: Name or NCBI Taxonomy ID of one or organisms. The web service currently provides interactions for human, mouse and rat. For other organisms, the data will be translated by orthologous gene pairs from human. In this case, only one organism can be provided. If miRNA, lncRNA or small molecule datasets included, orthology translation is not possible and will remove the interactions with non-protein partners.
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.
genesymbol_resource	Character: either "uniprot" or "ensembl". The former leaves intact the gene symbols returned by the web service, originally set from UniProt. The latter updates the gene symbols from Ensembl, which uses a slightly different gene symbol standard. In this case a few records will be duplicated, where Ensembl provides ambiguous translation.
types	Character: interaction types, such as "transcriptional", "post_transcriptional", "post_translational", etc.
...	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

• interaction_graph

• print_interactions

Examples

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

saezlab/OmnipathR documentation built on July 13, 2024, 6:18 p.m.