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Parse Mapping for Single Term (INTERNAL)

parse_term_mapping.Rd

Parses mappings generated by pyobo_map() or otherwise produced by the python module GILDA AT THE LEVEL of a single input term.

Usage

parse_term_mapping(
  py_gilda_term_mappings,
  best_only = TRUE,
  warn_best_gt1 = FALSE,
  ...
)

Arguments

py_gilda_term_mappings

A list of mappings between a single input term and one or more namespace terms (stored as specialized ScoredMatch python objects, as defined by GILDA; see extract_ScoredMatch).

best_only

Whether to return the best scoring result(s) only, as a boolean. FALSE will return all results. NOTE: TRUE will return more than one result in the case of ties.

warn_best_gt1

Whether to warn that best mapping ties exist for a term.

...

Arguments passed on to extract_ScoredMatch

prefix

Optional prefix to add to namespace local unique identifiers (LUI; e.g. 4, the LUI for "disease" in DO), as a string; preferably to create a complete namespace ID (e.g. "DOID:4").

prefix_sep

Optional separator placed between prefix and namespace LUIs, as a string. Ignored if prefix = NULL.

Value

List of data frames with the mapping result(s) for each term.