Functions for Reading Ontologies into R

Description

Functions for reading ontologies into R and manipulating sets of ontological terms.

Author(s)

Daniel Greene <dg333@cam.ac.uk>

Maintainer: Daniel Greene <dg333@cam.ac.uk>

References

Greene D, Richardson S, Turro E (2017). 'ontologyX: a suite of R packages for working with ontological data. _Bioinformatics_, 33(7), 1104–1106.

Westbury SK, Turro E, Greene D, Lentaigne C, Kelly AM, Bariana TK, Simeoni I, Pillois X, Attwood A, Austin S, Jansen SB, Bakchoul T, Crisp-Hihn A, Erber WN, Favier R, Foad N, Gattens M, Jolley JD, Liesner R, Meacham S, Millar CM, Nurden AT, Peerlinck K, Perry DJ, Poudel P, Schulman S, Schulze H, Stephens JC, Furie B, Robinson PN, Geet Cv, Rendon A, Gomez K, Laffan MA, Lambert MP, Nurden P, Ouwehand WH, Richardson S, Mumford AD and Freson K (2015). ‘Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders.’ _Genome Med_, *7*(1), pp. 36.

Kohler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jahn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Van Vooren S, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout A, de Leeuw N, de Vries B, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE and Robinson PN (2014). ‘The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.’ _Nucleic Acids Res._, *42*(Database issue), pp. D966-974.

Ashburner et al. Gene ontology: tool for the unification of biology (2000) Nat Genet 25(1):25-9

Smith, Cynthia L., Carroll-Ann W. Goldsmith, and Janan T. Eppig. ‘The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information.’ Genome biology 6.1 (2004): 1.

Case ontology_index object to data.frame

Description

Case ontology_index object to data.frame

Usage

## S3 method for class 'ontology_index'
as.data.frame(x, ...)

Arguments

Value

data.frame containing information about an ontology, rows corresponding to terms and columns to properties.

Check an ontology index object

Description

Perform simple consistency checks on ontology_index object

Usage

check(ontology, stop_if_invalid = FALSE)

Arguments

Exclude terms descending from any in a given set of root terms

Description

Exclude from set terms, any terms that are either in, or descend from one of, the set roots.

Usage

exclude_descendants(ontology, roots, terms)

Arguments

Value

Character vector of terms

See Also

intersection_with_descendants, prune_descendants

Get set of terms containing all ancestors of terms in a given set

Description

Get set of terms containing all ancestors of terms in a given set

Usage

get_ancestors(ontology, terms)

Arguments

Value

Character vector of all terms which are an ancestor of at least one term in terms, including the terms themselves

See Also

link{get_descendants}

Examples

data(hpo)
get_ancestors(hpo, c("HP:0001873", "HP:0011877"))

Get set of terms containing all descendants of terms in a given set

Description

Get set of terms containing all descendants of terms in a given set

Usage

get_descendants(ontology, roots, exclude_roots = FALSE)

Arguments

Value

Character vector of terms

See Also

link{get_ancestors}

Examples

data(hpo)
get_descendants(hpo, roots="HP:0001873")

Read ontology from OBO file into R

Description

Read ontology from OBO file into R

Usage

get_ontology(
  file,
  propagate_relationships = "is_a",
  extract_tags = "minimal",
  merge_equivalent_terms = TRUE
)

get_OBO(
  file,
  propagate_relationships = "is_a",
  extract_tags = "minimal",
  merge_equivalent_terms = TRUE
)

Arguments

Value

ontology_index object.

See Also

get_relation_names

Get names of relations used in OBO file

Description

Get names of relations used in OBO file

Usage

get_relation_names(file)

Arguments

See Also

get_ontology

Get logical descendancy matrix for set of terms

Description

Get logical descendancy matrix for set of terms

Usage

get_term_descendancy_matrix(ontology, terms = NULL, rows = terms, cols = terms)

Arguments

Value

A logical square matrix of with length(terms) columns and rows. result[row_term,col_term] == TRUE if row_term is an ancestor (and not the same as) of col_term.

A logical matrix.

Examples

data(hpo)
get_term_descendancy_matrix(hpo, c("HP:0001873", "HP:0011877"))

Get frequency of each term in a set of phenotypes

Description

Get frequency of each term in a set of phenotypes

Usage

get_term_frequencies(ontology, term_sets, patch_missing = FALSE)

Arguments

Value

Numeric vector of information contents, named by corresponding terms. Takes into account ancestors, in the sense that all ancestor terms implied by the phenotypes are considered 'on'

See Also

get_term_info_content

Examples

data(hpo)
get_term_frequencies(hpo, list("HP:0001873"))

Get information content of each term in a set of phenotypes

Description

Get information content of each term in a set of phenotypes

Usage

get_term_info_content(ontology, term_sets, patch_missing = FALSE)

Arguments

Value

Numeric vector of information contents, named by corresponding terms. Takes into account ancestors, in the sense that all ancestor terms implied by the phenotypes are considered 'on'

Examples

data(hpo)
get_term_info_content(hpo, list("HP:0001873"))

Get property of individual ontological term

Description

Get property of individual ontological term

Usage

get_term_property(ontology, property_name, term, as_names = FALSE)

Arguments

GO index

Description

ontology_index object encapsulating structure of the Gene Ontology (HPO) comprising a list of lists/vectors of properties of GO terms indexed by term ID (downloaded from https://current.geneontology.org/ontology/go-basic.obo).

Format

List of lists and vectors

HPO index

Description

ontology_index object encapsulating structure of the Human Phenotype Ontology (HPO) comprising a list of lists/vectors of properties of HPO terms indexed by term ID (downloaded from https://hpo.jax.org/app/data/ontology).

Format

List of lists and vectors

Intersect a set of terms with the descendants of a given set of roots

Description

Intersect a set of terms with the descendants of a given set of roots

Usage

intersection_with_descendants(ontology, roots, terms)

Arguments

Value

Character vector of terms

See Also

exclude_descendants, prune_descendants

Examples

data(hpo)
intersection_with_descendants(hpo, c("HP:0001872", "HP:0000707"), c("HP:0001873", "HP:0011877"))

Remove redundant/implied terms from a set of terms

Description

Remove redundant/implied terms from a set of terms

Usage

minimal_set(ontology, terms)

Arguments

Value

Character vector of terms

Examples

data(hpo)
minimal_set(hpo, c("HP:0001873", "HP:0001872"))

MPO index

Description

ontology_index object encapsulating structure of the Mammalian Phenotype Ontology (MPO) comprising a list of lists/vectors of properties of MPO terms indexed by term ID (downloaded from https://www.informatics.jax.org/downloads/reports/MPheno_OBO.ontology).

Format

List of lists and vectors

Create ontology_index object from vectors and lists of term properties

Description

Create ontology_index object from vectors and lists of term properties

Usage

ontology_index(
  parents,
  id = names(parents),
  name = id,
  obsolete = setNames(nm = id, rep(FALSE, length(id))),
  version = NULL,
  ...
)

Arguments

Examples

animal_superclasses <- list(animal=character(0), mammal="animal", cat="mammal", fish="animal")
animal_ontology <- ontology_index(parents=animal_superclasses)
unclass(animal_ontology)

Print ontology_index object

Description

Print ontology_index object

Usage

## S3 method for class 'ontology_index'
print(x, ...)

Arguments

Value

Prints a summary

Select terms by propagating relations from a set of terms

Description

An 'ontology_index' can contain multiple relations (for example in the case of the Gene Ontology, "is_a" and "part_of" could be stored as separate properties in an ‘ontology_index'). Transitive relations (i.e. relations such that x related to y and y related to z implies x related to z, for example the relation ’is an ancestor of') stored by an ‘ontology_index' can be propagated using this function. The ’inverse relations' (i.e. x inversely related to y if y related to x) can also be propagated by setting the use_inverse_relations parameter to TRUE.

Usage

propagate_relations(
  ontology,
  roots,
  relations,
  use_inverse_relations = FALSE,
  exclude_roots = FALSE
)

Arguments

Value

Character vector of terms

See Also

get_ancestors, get_descendants

Exclude terms descending from a given set of roots but include those roots which were originally implicitly present.

Description

Given two sets of terms, roots and terms, construct a set of terms containing those in terms which do not descend from any term in roots, and also any terms in roots which are ancestors of any term in terms.

Usage

prune_descendants(ontology, roots, terms)

Arguments

Value

Character vector of terms

See Also

exclude_descendants, intersection_with_descendants