gpt_annot_class: GPT annotations: add severity class

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

GPT annotations: add severity class

Description

Convert severity annotations ot severity classes (profound > severe > moderate > mild) to approximate those introduced in Lazarin et al. 2014.

Usage

gpt_annot_class(
  res_coded = gpt_annot_codify(),
  inclusion_values = c(2, 3),
  tiers_dict = list(death = 1, intellectual_disability = 1, impaired_mobility = 2,
    physical_malformations = 2, blindness = 3, sensory_impairments = 3, immunodeficiency
    = 3, cancer = 3, reduced_fertility = 4),
  add_severity_score_gpt = TRUE
)

Arguments

res_coded	The output of list gpt_annot_codify.
inclusion_values	Numerically encoded annotation values to count as hits. See the gpt_annot_codify(code_dict=) argument defaults for the mappings. Defaults to 2 ("often") and 3 ("always").
tiers_dict	A named list of severity tiers.
add_severity_score_gpt	Whether to add a continuous severity score as well.

Value

A data.table with severity classes, as well as severity scores (0-100) which can be used to rank severity within each class.

Examples

res_coded <- gpt_annot_codify()
res_class <- gpt_annot_class(res_coded)

neurogenomics/HPOExplorer documentation built on Aug. 24, 2024, 1:39 a.m.