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ontologyIndex (version 2.2)

Functions for Reading Ontologies into R

Description

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

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Version

Install

install.packages('ontologyIndex')

Monthly Downloads

1,542

Version

2.2

License

GPL (>= 2)

Maintainer

Daniel Greene

Last Published

October 28th, 2016

Functions in ontologyIndex (2.2)

get_term_descendancy_matrix

Get logical descendancy matrix for set of terms
get_OBO

Read ontology from OBO file into R
exclude_descendants

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

Get frequency of each term in a set of phenotypes
get_descendants

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

Read ontology as ontology_index from OWL format file
get_ontology

Read ontology from obo file into R
get_ancestors

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

Perform simple consistency checks on ontology_index object
get_term_info_content

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

Remove redundant/implied terms 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
ontology_index

Create ontology_index object from vectors and lists of term properties
get_term_property

Get property of individual ontological term
mpo

MPO index
OWL_list_attributes

Create lists of attributes per node in OWL file
OWL_properties

Get vectors of term properties from set of OWL nodes
print.ontology_index

Print ontology_index object.
prune_descendants

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