Filter functions

Source: R/0docs.R, R/filter_descendants.R

Functions to filter data.table objects.

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")
#> Reading cached RDS file: phenotype_to_genes.txt
#> + Version: v2024-04-26
#> Extracting data for 23 descendents.
#> Computing gene counts.
#> Adding term definitions.
#> Adding level-2 ancestor to each HPO ID.
#> Adding ancestor metadata.
#> Ancestor metadata already present. Use force_new=TRUE to overwrite.
#> 23 associations remain after filtering.
#> Getting absolute ontology level for 18,536 IDs.
#> Computing ontology level / gene count ratio.
phenos2 <- filter_descendants(phenos = phenos,
                              keep_descendants = "Motor delay")
#> Translating ontology terms to ids.
#> Keeping descendants of 1 term(s).
#> 10 terms remain after filtering.
#> 9 associations remain after filtering.