oma_pairwise_translated: Orthologous pairs between two organisms for ID types not...

In saezlab/OmnipathR: OmniPath web service client and more

Orthologous pairs between two organisms for ID types not supported by OMA

Description

The Orthologous Matrix (OMA), a resource of orthologous relationships between genes, doesn't provide gene symbols, the identifier preferred in many bioinformatics pipelines. Hence this function wraps oma_pairwise by translating the identifiers used in OMA to gene symbols. Items that can not be translated to 'id_type' (but present in the data with their internal OMA IDs) will be removed. Then, in this function we translate the identifiers to the desired ID type.

Usage

oma_pairwise_translated(
  organism_a = "human",
  organism_b = "mouse",
  id_type = "uniprot",
  oma_id_type = "uniprot_entry",
  mappings = c("1:1", "1:m", "n:1", "n:m"),
  only_ids = TRUE
)

Arguments

organism_a	Name or identifier of an organism.
organism_b	Name or identifier of another organism.
id_type	The gene or protein identifier to use in the table. For a list of supported ID types see 'omnipathr.env$id_types$oma'. These are the identifiers that will be translated to gene symbols.
oma_id_type	Character: the gene or protein identifier to be queried from OMA. These IDs will be translated to 'id_type'.
mappings	Character vector: control ambiguous mappings: 1:1 - unambiguous 1:m - one-to-many n:1 - many-to-one n:m - many-to-many
only_ids	Logical: include only the two identifier columns, not the mapping type and the orthology group columns.

Value

A data frame with orthologous gene pairs.

Examples

oma_pairwise_translated("human", "mouse")

saezlab/OmnipathR documentation built on Oct. 16, 2024, 11:49 a.m.