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Ortholog backend backed by babelgene

Source: R/orthologs.R
ortholog_babelgene.Rd

Gene-ortholog backend using the offline babelgene package, which ships precomputed orthologs between human and a range of model organisms. This is the default backend for ortholog_genes().

Usage

ortholog_babelgene(features, from, to, gene_col, id_type, cache = NULL, ...)

Arguments

features

A tibble of features with a gene column and a .feature_id key (supplied by ortholog_genes()).

from, to

Source and target species (e.g. "human", "mouse", "rat"). babelgene is human-centric, so model-to-model mappings (e.g. rat-to-mouse) are routed through human.

gene_col

Name of the gene-identifier column.

id_type

One of "symbol", "entrez", "ensembl".

cache

Optional path to a TSV file caching prior lookups. When given, a gene already in the file is read from there instead of queried again, and a newly queried gene is appended for next time. The cache is shared across from/to/id_type combinations in one file.

...

Passed to babelgene::orthologs() (e.g. min_support, top).

Value

A list with mapped and unmapped tibbles.

See also

ortholog_genes()

Examples

if (requireNamespace("babelgene", quietly = TRUE)) {
  feats <- tibble::tibble(gene = c("TP53", "MYC"), .feature_id = 1:2)
  out <- ortholog_babelgene(
    feats,
    from = "human",
    to = "mouse",
    gene_col = "gene",
    id_type = "symbol"
  )
  out$mapped
}
#> # A tibble: 2 × 3
#>   gene  .feature_id ortholog
#>   <chr>       <int> <chr>   
#> 1 TP53            1 Trp53   
#> 2 MYC             2 Myc