Learn R Programming
⚠️There's a newer version (2.9) of this package.Take me there.

ontologySimilarity (version 2.3)

Functions for Calculating Ontological Similarities

Description

Functions for calculating semantic similarities between ontological terms or sets of ontological terms based on term information content and assessing statistical significance of similarity in the context of a collection of sets of ontological terms.

Copy Link

Version

Install

install.packages('ontologySimilarity')

Monthly Downloads

289

Version

2.3

License

GPL (>= 2)

Maintainer

Daniel Greene

Last Published

December 19th, 2019

Functions in ontologySimilarity (2.3)

descendants_IC

Get information content based on number of descendants each term has
get_sim

Calculate the group similarity of a set of row/column indices
get_sim_grid

Get similarity matrix of pairwise similarities of term sets.
get_similarity_rank_matrix

Get matrix of similarity rank from similarity matrix
get_profile_sims

Get similarities of term sets to profile
get_term_set_to_term_sims

Get `term sets to term' similarity matrix
GO_IC

Gene Ontology terms information content.
create_sim_index

Create light-weight similarity index for fast lookups of between term set similarity.
sample_group_sim_from_ontology

Draw sample of group similarities for groups of given size based on ontology argument
sample_group_sim

Draw sample of group similarities of groups of given size
get_term_sim_mat

Get term-term similarity matrix
lin

Calculate Lin similarity score of two term sets
get_sim_p

Get similarity p-value
get_sim_p_from_ontology

Get similarity p-value for subgroup of list of term sets
ontologySimilarity-package

Functions for Calculating Ontological Similarities
resnik

Calculate Resnik similarity score of two term sets
get_asym_sim_grid

Get asymmetrical similarity matrix
gene_GO_terms

Gene Ontology annotation of genes