ontologySimilarity: Functions for Calculating Ontological Similarities

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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.

Author
Daniel Greene
Date of publication
2016-10-28 01:14:47
Maintainer
Daniel Greene <dg333@cam.ac.uk>
License
GPL (>= 2)
Version
2.2

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Man pages

create_sim_index
Create light-weight similarity index for fast lookups of...
descendants_IC
Get information content based on number of descendants each...
gene_GO_terms
Gene Ontology annotation of genes
get_asym_sim_grid
Get asymmetrical similarity matrix
get_profile_sims
Get similarities of term sets to profile
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_sim_p
Get similarity p-value
get_sim_p_from_ontology
Get similarity p-value for subgroup of list of term sets
get_term_set_to_term_sims
Get 'term sets to term' similarity matrix
get_term_sim_mat
Get term-term similarity matrix
GO_IC
Gene Ontology terms information content.
lin
Calculate Lin similarity score of two term sets
ontologySimilarity-package
Functions for Calculating Ontological Similarities
resnik
Calculate Resnik similarity score of two term sets
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...

Files in this package

ontologySimilarity
ontologySimilarity/inst
ontologySimilarity/inst/doc
ontologySimilarity/inst/doc/ontologySimilarity-GO-example.R
ontologySimilarity/inst/doc/ontologySimilarity-examples.html
ontologySimilarity/inst/doc/ontologySimilarity-GO-example.Rmd
ontologySimilarity/inst/doc/ontologySimilarity-introduction.html
ontologySimilarity/inst/doc/ontologySimilarity-introduction.Rmd
ontologySimilarity/inst/doc/ontologySimilarity-GO-example.html
ontologySimilarity/inst/doc/ontologySimilarity-introduction.R
ontologySimilarity/inst/doc/ontologySimilarity-examples.Rmd
ontologySimilarity/inst/doc/ontologySimilarity-examples.R
ontologySimilarity/src
ontologySimilarity/src/TermList.cpp
ontologySimilarity/src/TermSetSimData.h
ontologySimilarity/src/Interface.h
ontologySimilarity/src/PVal.cpp
ontologySimilarity/src/Sampling.h
ontologySimilarity/src/SimMatrix.cpp
ontologySimilarity/src/PVal.h
ontologySimilarity/src/RcppExports.cpp
ontologySimilarity/src/TermSetSimData.cpp
ontologySimilarity/src/Sampling.cpp
ontologySimilarity/src/SimMatrix.h
ontologySimilarity/src/Interface.cpp
ontologySimilarity/src/TermList.h
ontologySimilarity/NAMESPACE
ontologySimilarity/data
ontologySimilarity/data/GO_IC.RData
ontologySimilarity/data/gene_GO_terms.RData
ontologySimilarity/R
ontologySimilarity/R/group-sim.R
ontologySimilarity/R/term-set-sim.R
ontologySimilarity/R/data.R
ontologySimilarity/R/functions.R
ontologySimilarity/R/RcppExports.R
ontologySimilarity/vignettes
ontologySimilarity/vignettes/ontologySimilarity-GO-example.Rmd
ontologySimilarity/vignettes/ontologySimilarity-introduction.Rmd
ontologySimilarity/vignettes/ontologySimilarity-examples.Rmd
ontologySimilarity/MD5
ontologySimilarity/build
ontologySimilarity/build/vignette.rds
ontologySimilarity/DESCRIPTION
ontologySimilarity/man
ontologySimilarity/man/get_profile_sims.Rd
ontologySimilarity/man/sample_group_sim_from_ontology.Rd
ontologySimilarity/man/gene_GO_terms.Rd
ontologySimilarity/man/get_term_set_to_term_sims.Rd
ontologySimilarity/man/get_sim.Rd
ontologySimilarity/man/get_sim_grid.Rd
ontologySimilarity/man/GO_IC.Rd
ontologySimilarity/man/get_sim_p.Rd
ontologySimilarity/man/descendants_IC.Rd
ontologySimilarity/man/sample_group_sim.Rd
ontologySimilarity/man/get_sim_p_from_ontology.Rd
ontologySimilarity/man/get_asym_sim_grid.Rd
ontologySimilarity/man/get_similarity_rank_matrix.Rd
ontologySimilarity/man/get_term_sim_mat.Rd
ontologySimilarity/man/lin.Rd
ontologySimilarity/man/resnik.Rd
ontologySimilarity/man/ontologySimilarity-package.Rd
ontologySimilarity/man/create_sim_index.Rd