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_genesymbolswill 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.
Examples
oma_pairwise("human", "mouse", "uniprot")
#> Error in rename(., `:=`(!!sym(to_col), To)): Names must be unique.
#> ✖ These names are duplicated:
#> * "id_organism_a" at locations 1 and 3.
# # 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