ontologyIndex: Functions for Reading Ontologies into R

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

Author
Daniel Greene <dg333@cam.ac.uk>
Date of publication
2016-11-24 00:17:34
Maintainer
Daniel Greene <dg333@cam.ac.uk>
License
GPL (>= 2)
Version
2.3

View on CRAN

Man pages

check
Perform simple consistency checks on 'ontology_index' object
exclude_descendants
Exclude terms descending from any in a given set of root...
get_ancestors
Get set of terms containing all ancestors of terms in a given...
get_descendants
Get set of terms containing all descendants of terms in a...
get_ontology
Read ontology from OBO file into R
get_relation_names
Get names of relations used in OBO file
get_term_descendancy_matrix
Get logical descendancy matrix for set of terms
get_term_frequencies
Get frequency of each term in a set of phenotypes
get_term_info_content
Get information content of each term in a set of phenotypes
get_term_property
Get property of individual ontological term
go
GO index
hpo
HPO index
intersection_with_descendants
Intersect a set of terms with the descendants of a given set...
minimal_set
Remove redundant/implied terms from a set of terms
mpo
MPO index
ontology_index
Create 'ontology_index' object from vectors and lists of term...
ontologyIndex-package
Functions for Reading Ontologies into R
print.ontology_index
Print 'ontology_index' object.
propagate_relations
Select terms by propagating relations from a set of terms
prune_descendants
Exclude terms descending from a given set of roots but...

Files in this package

ontologyIndex
ontologyIndex/inst
ontologyIndex/inst/doc
ontologyIndex/inst/doc/intro-to-ontologyX.html
ontologyIndex/inst/doc/reading-ontologies.html
ontologyIndex/inst/doc/reading-ontologies.R
ontologyIndex/inst/doc/reading-ontologies.Rmd
ontologyIndex/inst/doc/intro-to-ontologyX.Rmd
ontologyIndex/inst/doc/intro-to-ontologyX.R
ontologyIndex/NAMESPACE
ontologyIndex/NEWS.md
ontologyIndex/data
ontologyIndex/data/mpo.RData
ontologyIndex/data/hpo.RData
ontologyIndex/data/datalist
ontologyIndex/data/go.RData
ontologyIndex/R
ontologyIndex/R/sets.R
ontologyIndex/R/generic.R
ontologyIndex/R/data.R
ontologyIndex/R/descendants.R
ontologyIndex/vignettes
ontologyIndex/vignettes/reading-ontologies.Rmd
ontologyIndex/vignettes/intro-to-ontologyX.Rmd
ontologyIndex/MD5
ontologyIndex/build
ontologyIndex/build/vignette.rds
ontologyIndex/DESCRIPTION
ontologyIndex/man
ontologyIndex/man/get_ancestors.Rd
ontologyIndex/man/intersection_with_descendants.Rd
ontologyIndex/man/hpo.Rd
ontologyIndex/man/minimal_set.Rd
ontologyIndex/man/get_term_property.Rd
ontologyIndex/man/get_relation_names.Rd
ontologyIndex/man/prune_descendants.Rd
ontologyIndex/man/ontology_index.Rd
ontologyIndex/man/get_term_info_content.Rd
ontologyIndex/man/propagate_relations.Rd
ontologyIndex/man/go.Rd
ontologyIndex/man/ontologyIndex-package.Rd
ontologyIndex/man/mpo.Rd
ontologyIndex/man/check.Rd
ontologyIndex/man/get_ontology.Rd
ontologyIndex/man/print.ontology_index.Rd
ontologyIndex/man/get_descendants.Rd
ontologyIndex/man/exclude_descendants.Rd
ontologyIndex/man/get_term_frequencies.Rd
ontologyIndex/man/get_term_descendancy_matrix.Rd