gpt_annot_codify: Check annotations from GPT

In neurogenomics/HPOExplorer: Analysis and Visualisation of the Human Phenotype Ontology

Check annotations from GPT

Description

Check GPT phenotype annotations using a several metrics.

Usage

gpt_annot_codify(
  annot = gpt_annot_read(),
  remove_duplicates = TRUE,
  code_dict = c(never = 0, rarely = 1, often = 2, always = 3),
  weights_dict = list(death = 6, intellectual_disability = 5, impaired_mobility = 4,
    physical_malformations = 3, blindness = 4, sensory_impairments = 3, immunodeficiency
    = 3, cancer = 3, reduced_fertility = 1, congenital_onset = 1),
  reset_weights_dict = FALSE,
  filters = list()
)

Arguments

annot	GPT-generated phenotype annotations.
remove_duplicates	Ensure only 1 row per phenotype.
code_dict	Numerical encodings of annotation values.
weights_dict	Weights to be applied to each annotation metric.
reset_weights_dict	Override weights_dict values and set all values to 1. This will ensure that all annotations are unweighted.
filters	A named list, where each element in the list is the name of a column in the data, and the vector within each element represents the values to include in the final data.

Value

Named list

Examples

res_coded <- gpt_annot_codify()

neurogenomics/HPOExplorer documentation built on April 17, 2025, 9:25 p.m.