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ontologyIndex (version 2.12)

Reading Ontologies into R

Description

Functions for reading ontologies into R as lists and manipulating sets of ontological terms - 'ontologyX: A suite of R packages for working with ontological data', Greene et al 2017 .

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Version

Install

install.packages('ontologyIndex')

Monthly Downloads

1,319

Version

2.12

License

GPL (>= 2)

Maintainer

Daniel Greene

Last Published

February 27th, 2024

Functions in ontologyIndex (2.12)

prune_descendants

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

Create ontology_index object from vectors and lists of term properties
as.data.frame.ontology_index

Case ontology_index object to data.frame
get_term_frequencies

Get frequency of each term in a set of phenotypes
exclude_descendants

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

Get names of relations used in OBO file
get_ontology

Read ontology from OBO file into R
check

Check an ontology index object
get_ancestors

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

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

Get logical descendancy matrix for set of terms
get_term_info_content

Get information content of each term in a set of phenotypes
mpo

MPO index
minimal_set

Remove redundant/implied terms from a set of terms
print.ontology_index

Print ontology_index object
get_term_property

Get property of individual ontological term
propagate_relations

Select terms by propagating relations from a set of terms
hpo

HPO index
go

GO index
ontologyIndex-package

Functions for Reading Ontologies into R
intersection_with_descendants

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