This function applies validation to ensure only legitimate biomedical entities are included, while preserving trusted terms.
Usage
valid_entities(
entities,
primary_term,
primary_term_variations = NULL,
validation_function = NULL,
verbose = TRUE,
entity_col = "entity",
type_col = "entity_type"
)Arguments
- entities
Data frame of entities to filter
- primary_term
The primary term to trust
- primary_term_variations
Vector of variations of the primary term to trust
- validation_function
Function to validate entities (default: is_valid_biomedical_entity)
- verbose
Logical; if TRUE, print status messages (default: TRUE)
- entity_col
Name of the column containing entity names (default: "entity")
- type_col
Name of the column containing entity types (default: "entity_type")
Examples
# Create example entities
entities <- data.frame(
entity = c("migraine", "optimization", "receptor", "europe"),
entity_type = c("disease", "process", "protein", "location")
)
# Validate entities
validated <- valid_entities(entities, "migraine", c("migrain", "headache"))
#> Filtered from 4 to 2 validated entities
print(validated)
#> entity entity_type
#> 1 migraine disease
#> 2 receptor protein