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Deprecated alias for translate()

Source: R/orthologize.R
orthologize.Rd

orthologize() is the earlier name for translate(). It still works and calls translate() with the same arguments, and warns once per session. New code should call translate() directly.

Usage

orthologize(x, to, from = NULL, ...)

Arguments

x

The thing to translate. Either:

  • a data.frame/tibble of features, or

  • a Cohort object.

to

Character scalar naming the target species/assembly.

from

For a feature table, a character scalar naming the source species/assembly; required for the "ortholog" strategy, optional (recorded as provenance) for "liftover". For a Cohort, NULL (default) infers the source species from subject_tbl$species: used directly when the cohort has one species, or resolved per analysis (and, for an analysis with a subject_id column, per subject) when it has more than one. Give it explicitly to override inference.

...

Strategy-specific arguments. For a feature table:

  • strategy: "liftover" (coordinate features; see liftover_intervals()) or "ortholog" (gene features; see ortholog_genes()).

  • chain: chain-file path for "liftover".

  • backend: translation backend (defaults: "rtracklayer" for liftover, "babelgene" for ortholog).

  • plus backend arguments such as gene_col/id_type for orthologs.

For a Cohort:

  • chain: chain-file path used for any feature_type = "interval" analysis. A cohort translated from more than one source species can pass a named list instead, one chain per source species (e.g. list(rat = "rn7ToHg38.chain", mouse = "mm39ToHg38.chain")).

  • liftover_backend, ortholog_backend: backends for the two feature kinds.

  • analyses: optional character vector restricting which analyses to translate (defaults to all that have a registered spec with a feature_type).

Value

See translate().

See also

translate()