Get the most severe phenotypes per severity class: Profound, Severe, Moderate, Mild. The exception to this is the "Mild" class, where the least severe phenotypes will be taken instead of the most severe phenotypes.
get_top_phenos(
res_class = gpt_annot_class(),
keep_ont_levels = seq(3, 17),
keep_descendants = "Phenotypic abnormality",
n_per_class = 10,
annotation_order = NULL,
split_by_congenital = TRUE
)Output of the gpt_annot_class function.
Only keep phenotypes at certain absolute ontology levels to keep. See add_ont_lvl for details.
Terms whose descendants should be kept
(including themselves).
Set to NULL (default) to skip this filtering step.
Number of phenotypes per severity class to include.
The order of the annotations to include.
Split the phenotypes by congenital onset (congenital = always/often, noncongenital = never/rarely).
top_phenos <- get_top_phenos()
#> Translating ontology terms to ids.
#> Reading cached RDS file: phenotype_to_genes.txt
#> + Version: v2024-12-12
#> 383 phenotypes do not have matching HPO IDs.
#> Reading in GPT annotations for 16,753 phenotypes.
#> Assigning severity classes.
#> Adding level-2 ancestor to each HPO ID.
#> Adding ancestor metadata.
#> Ancestor metadata already present. Use force_new=TRUE to overwrite.
#> Translating ontology terms to ids.
#> Keeping descendants of 1 term(s).
#> 18,379 terms remain after filtering.
#> 164,385 associations remain after filtering.
#> Getting absolute ontology level for 19,025 IDs.