filter_: Filter functions

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

Filter functions

Description

Functions to filter data.table objects.

Usage

filter_descendants(
  phenos,
  keep_descendants = NULL,
  remove_descendants = NULL,
  hpo = get_hpo()
)

Arguments

phenos	A data.table containing HPO IDs and other metadata.
keep_descendants	Terms whose descendants should be kept (including themselves). Set to NULL (default) to skip this filtering step.
remove_descendants	Terms whose descendants should be removed (including themselves). Set to NULL (default) to skip this filtering step.
hpo	Human Phenotype Ontology object, loaded from get_ontology.

Value

Filtered data.

data.table of phenotypes, with additional columns: "ancestor", "ancestor_id"

Functions

• filter_descendants(): filter_ Filter descendants

  Subset a phenos data.table to only descendants of an ancestor HPO ID term.

Examples

phenos <- make_phenos_dataframe(ancestor = "Neurodevelopmental delay")
phenos2 <- filter_descendants(phenos = phenos,
                              keep_descendants = "Motor delay")

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