Register a gene-ortholog backend

Adds a named ortholog backend so it can be selected by name in ortholog_genes(). A backend performs gene-level cross-species mapping; this pluggable design mirrors the liftover backends used for coordinate features.

Usage

register_ortholog_backend(name, fn)

Arguments

name

Character scalar naming the backend.

fn

A function with signature function(features, from, to, gene_col, id_type, ...) returning a list with two tibbles:

• mapped: input rows that had at least one ortholog, carrying the .feature_id key and an ortholog column with the target-species id.

• unmapped: input rows (carrying .feature_id) with no ortholog.

Value

Invisibly, the backend name.

See also

ortholog_backends(), ortholog_genes(), ortholog_babelgene()

Examples

# A backend that upper-cases rodent symbols into human ones, used by name.
to_upper <- function(features, from, to, gene_col, id_type, ...) {
  mapped <- features
  mapped$ortholog <- toupper(mapped[[gene_col]])
  list(mapped = mapped, unmapped = features[0, , drop = FALSE])
}
register_ortholog_backend("to_upper", to_upper)
"to_upper" %in% ortholog_backends()
#> [1] TRUE

genes <- data.frame(gene = c("Tp53", "Myc"))
ortholog_genes(genes, from = "rat", to = "human", backend = "to_upper")
#> 
#> ── TranslationResult (rat -> human, backend: to_upper) 
#> • input: 2
#> ✔ mapped: 2 (100%)
#> ✖ unmapped: 0
#> ! multi: 0