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ontologySimilarity (version 2.5)

Calculating Ontological Similarities

Description

Calculate similarity between ontological terms and sets of ontological terms based on term information content and assess statistical significance of similarity in the context of a collection of terms sets - Greene et al. 2017 .

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Version

Install

install.packages('ontologySimilarity')

Monthly Downloads

289

Version

2.5

License

GPL (>= 2)

Maintainer

Daniel Greene

Last Published

February 10th, 2021

Functions in ontologySimilarity (2.5)

get_similarity_rank_matrix

Get matrix of similarity rank from similarity matrix

lin

Calculate Lin similarity score of two term sets

get_term_sim_mat

Get term-term similarity matrix

get_term_set_to_term_sims

Get `term sets to term' similarity matrix

sample_group_sim

Draw sample of group similarities of groups of given size

sample_group_sim_from_ontology

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

get_sim_p_from_ontology

resnik

Calculate Resnik similarity score of two term sets

ontologySimilarity-package

Functions for Calculating Ontological Similarities

get_asym_sim_grid

Get asymmetrical similarity matrix

GO_IC

Gene Ontology terms information content.

gene_GO_terms

Gene Ontology annotation of genes

get_sim

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

descendants_IC

Get information content based on number of descendants each term has

get_sim_p

Get similarity p-value

create_sim_index

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

get_sim_grid

get_profile_sims