oma_pairwise: Orthologous gene pairs between two organisms
In saezlab/OmnipathR: OmniPath web service client and more

oma_pairwise

R Documentation

Orthologous gene pairs between two organisms

Description

From the web API of Orthologous Matrix (OMA). Items which could not be translated to 'id_type' (but present in the data with their internal OMA IDs) are removed.

Usage

oma_pairwise(
  organism_a = "human",
  organism_b = "mouse",
  id_type = "uniprot",
  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'. In addition, "genesymbol" is supported, in this case `oma_pairwise_genesymbols` will be called automatically.
`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("human", "mouse", "uniprot")
# # A tibble: 21,753 × 4
#    id_organism_a id_organism_b mapping oma_group
#    <chr>         <chr>         <chr>       <dbl>
#  1 Q15326        Q8R5C8        1:1       1129380
#  2 Q9Y2E4        B2RQ71        1:1        681224
#  3 Q92615        Q6A0A2        1:1       1135087
#  4 Q9BZE4        Q99ME9        1:1       1176239
#  5 Q9BXS1        Q8BFZ6        1:m            NA
# # … with 21,743 more rows

saezlab/OmnipathR documentation built on Nov. 10, 2024, 11:02 p.m.