oma_pairwise("human", "mouse", "uniprot")
-#> # A tibble: 21,753 × 2
+#> # A tibble: 13,006 × 2
#> id_organism_a id_organism_b
#> <chr> <chr>
-#> 1 Q15326 Q8R5C8
-#> 2 Q9Y2E4 B2RQ71
-#> 3 Q92615 Q6A0A2
-#> 4 Q9BZE4 Q99ME9
-#> 5 Q9BXS1 Q8BFZ6
-#> 6 Q9BXS1 Q8BFZ6
-#> 7 Q9Y2I8 Q8CBE3
-#> 8 Q9NS39 Q9JI20
-#> 9 Q01813 Q9WUA3
-#> 10 Q5JRX3 Q8K411
-#> # ℹ 21,743 more rows
+#> 1 P21452 P30549
+#> 2 Q8TAD7 P0C913
+#> 3 Q8N392 Q8K0Q5
+#> 4 O60285 Q641K5
+#> 5 Q07065 Q8BMK4
+#> 6 P78371 P80314
+#> 7 Q8N4U5 Q8K1H7
+#> 8 Q8WU20 Q8C180
+#> 9 O95619 Q9CR11
+#> 10 Q9NW08 P59470
+#> # ℹ 12,996 more rows
# # A tibble: 21,753 × 4
# id_organism_a id_organism_b mapping oma_group
# <chr> <chr> <chr> <dbl>
diff --git a/docs/reference/oma_pairwise_genesymbols.html b/docs/reference/oma_pairwise_genesymbols.html
index 984f6baf..3e764835 100644
--- a/docs/reference/oma_pairwise_genesymbols.html
+++ b/docs/reference/oma_pairwise_genesymbols.html
@@ -4,13 +4,13 @@
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. This part is done by . Then,
+in the data with their internal OMA IDs) will be removed. Then,
in this function we translate the identifiers to gene symbols.">Orthologous pairs of gene symbols between two organisms — oma_pairwise_genesymbols • OmnipathROrthologous pairs between two organisms for ID types not supported by OMA — oma_pairwise_translated • OmnipathR
+ Skip to contents
+
+
+
+
+
+
+
+
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 `omnipath.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")
+#> # A tibble: 13,006 × 2
+#> id_organism_a id_organism_b
+#> <chr> <chr>
+#> 1 P21452 P30549
+#> 2 Q8TAD7 P0C913
+#> 3 Q8N392 Q8K0Q5
+#> 4 O60285 Q641K5
+#> 5 Q07065 Q8BMK4
+#> 6 P78371 P80314
+#> 7 Q8N4U5 Q8K1H7
+#> 8 Q8WU20 Q8C180
+#> 9 O95619 Q9CR11
+#> 10 Q9NW08 P59470
+#> # ℹ 12,996 more rows
+
+
+
+
+
+