main: Main functions

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

Main functions

Description

Main functions.

Usage

annotate_phenos(
  phenos,
  hpo = get_hpo(),
  add_ont_lvl_absolute = TRUE,
  add_ont_lvl_relative = FALSE,
  add_info_content = TRUE,
  add_description = TRUE,
  add_disease_data = FALSE,
  add_ndiseases = add_disease_data,
  add_onsets = add_disease_data,
  add_deaths = add_disease_data,
  add_pheno_frequencies = add_disease_data,
  add_tiers = add_disease_data,
  add_severities = add_disease_data,
  add_disease_definitions = add_disease_data,
  include_mondo = FALSE,
  add_hoverboxes = FALSE,
  columns = list_columns(),
  interactive = TRUE
)

example_phenos(i = seq(10), hpo = get_hpo())

Arguments

phenos	A data.table containing HPO IDs and other metadata.
hpo	Human Phenotype Ontology object, loaded from get_ontology.
add_ont_lvl_absolute	Add the absolute ontology level of each HPO term. See get_ontology_levels for more details.
add_ont_lvl_relative	Add the relative ontology level of each HPO term. See get_ontology_levels for more details.
add_info_content	Add information content column for each phenotype.
add_description	Whether to get the phenotype descriptions as well (slower).
add_disease_data	Add all disease metadata columns. This will expand the data using allow.cartesian=TRUE.
add_ndiseases	Add the number of diseases per phenotype.
add_onsets	Add age of onset columns using add_onset.
add_deaths	Add age of death columns using add_death.
add_pheno_frequencies	Add the frequency of each phenotype in each disease.
add_tiers	Add severity Tiers column using add_tier.
add_severities	Add severity column using add_severity.
add_disease_definitions	Add disease definitions.
include_mondo	Add MONDO IDs, names, and definitions to each disease.
add_hoverboxes	Add hoverdata with add_hoverboxes.
columns	A named vector of columns in phenos to add to the hoverdata via add_hoverboxes.
interactive	Make the plot interactive.
i	Indices of HPO IDs to use.

Value

Data.

phenotype data.table

Functions

• annotate_phenos(): main Annotate phenotypes

  Annotate phenotypes data.table without various types of metadata.

• example_phenos(): main Example phenotypes dataframe

  Create a minimal example of a phenos dataframe.

Examples

phenos <- example_phenos()
phenos2 <- annotate_phenos(phenos)
phenos <- example_phenos()

neurogenomics/HPOExplorer documentation built on July 17, 2024, 3:12 p.m.