collectri: TF-target interactions from CollecTRI

In saezlab/OmnipathR: OmniPath web service client and more

TF-target interactions from CollecTRI

Description

CollecTRI is a comprehensive resource of transcriptional regulation, published in 2023, consisting of 14 resources and original literature curation.

Usage

collectri(
  resources = NULL,
  organism = 9606L,
  references_by_resource = TRUE,
  exclude = NULL,
  strict_evidences = TRUE,
  genesymbol_resource = NULL,
  ...
)

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.
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.
exclude	Character: datasets or resources to exclude.
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. In case of CollecTRI this is not desirable for most of the applications. For most of the other interaction querying functions it is 'FALSE' by default.
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.
...	Optional additional arguments, passed to import_transcriptional_interactions.

Value

A dataframe of TF-target interactions.

See Also

• import_transcriptional_interactions

• dorothea

• get_interaction_resources

• import_all_interactions

• interaction_graph

• print_interactions

Examples

collectri_grn <- collectri()
collectri_grn

saezlab/OmnipathR documentation built on June 17, 2024, 2:24 a.m.