ontologyIndex: Functions for Reading Ontologies into R
Version 2.4

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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AuthorDaniel Greene <dg333@cam.ac.uk>
Date of publication2017-02-06 14:21:31
MaintainerDaniel Greene <dg333@cam.ac.uk>
LicenseGPL (>= 2)
Version2.4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ontologyIndex")

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...

Functions

ancs_from_pars Source code
as.data.frame.ontology_index Source code
check Man page Source code
exclude_descendants Man page Source code
get_OBO Man page
get_ancestors Man page Source code
get_descendants Man page Source code
get_ontology Man page Source code
get_relation_names Man page Source code
get_term_descendancy_matrix Man page Source code
get_term_frequencies Man page Source code
get_term_info_content Man page Source code
get_term_property Man page Source code
go Man page
hpo Man page
intersection_with_descendants Man page Source code
minimal_set Man page Source code
mpo Man page
ontologyIndex Man page
ontologyIndex-package Man page
ontology_index Man page Source code
print.ontology_index Man page Source code
propagate_relations Man page Source code
prune_descendants Man page Source code
str_ancs_from_pars Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/intro-to-ontologyX.html
inst/doc/reading-ontologies.html
inst/doc/reading-ontologies.R
inst/doc/reading-ontologies.Rmd
inst/doc/intro-to-ontologyX.Rmd
inst/doc/intro-to-ontologyX.R
NAMESPACE
NEWS.md
data
data/mpo.RData
data/hpo.RData
data/datalist
data/go.RData
R
R/sets.R
R/generic.R
R/data.R
R/descendants.R
vignettes
vignettes/reading-ontologies.Rmd
vignettes/intro-to-ontologyX.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/get_ancestors.Rd
man/intersection_with_descendants.Rd
man/hpo.Rd
man/minimal_set.Rd
man/get_term_property.Rd
man/get_relation_names.Rd
man/prune_descendants.Rd
man/ontology_index.Rd
man/get_term_info_content.Rd
man/propagate_relations.Rd
man/go.Rd
man/ontologyIndex-package.Rd
man/mpo.Rd
man/check.Rd
man/get_ontology.Rd
man/print.ontology_index.Rd
man/get_descendants.Rd
man/exclude_descendants.Rd
man/get_term_frequencies.Rd
man/get_term_descendancy_matrix.Rd
ontologyIndex documentation built on May 20, 2017, 3:24 a.m.