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 gene symbols.
Usage
oma_pairwise_genesymbols(
organism_a = "human",
organism_b = "mouse",
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.
- 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.
Examples
oma_pairwise_genesymbols("human", "mouse")
#> # A tibble: 12,905 × 2
#> id_organism_a id_organism_b
#> <chr> <chr>
#> 1 TACR2 Tacr2
#> 2 ARHGAP18 Arhgap18
#> 3 NUAK1 Nuak1
#> 4 CKAP4 Ckap4
#> 5 CCT2 Cct2
#> 6 TCP11L2 Tcp11l2
#> 7 FRS2 Frs2
#> 8 YEATS4 Yeats4
#> 9 POLR3B Polr3b
#> 10 LAMA2 Lama2
#> # ℹ 12,895 more rows