get_top_phenos: Get top phenotypes

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

Get top phenotypes

Description

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.

Usage

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
)

Arguments

res_class	Output of the gpt_annot_class function.
keep_ont_levels	Only keep phenotypes at certain absolute ontology levels to keep. See add_ont_lvl for details.
keep_descendants	Terms whose descendants should be kept (including themselves). Set to NULL (default) to skip this filtering step.
n_per_class	Number of phenotypes per severity class to include.
annotation_order	The order of the annotations to include.
split_by_congenital	Split the phenotypes by congenital onset (congenital = always/often, noncongenital = never/rarely).

Examples

top_phenos <- get_top_phenos()

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