ontologySimilarity: Functions for Calculating Ontological Similarities
Version 2.2

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.

Browse man pages Browse package API and functions Browse package files

AuthorDaniel Greene
Date of publication2016-10-28 01:14:47
MaintainerDaniel Greene <dg333@cam.ac.uk>
LicenseGPL (>= 2)
Version2.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ontologySimilarity")

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...

Functions

GO_IC Man page
calc_term_sim_mat Source code
check_pop_sim_class Source code
components_for_calc_sim_from_ic Source code
create_sim_index Man page Source code
descendants_IC Man page Source code
gene_GO_terms Man page
get_asym_sim_grid Man page Source code
get_c_group_inds Source code
get_profile_sims Man page Source code
get_sim Man page Source code
get_sim.default Man page Source code
get_sim.integer Man page Source code
get_sim.matrix Man page Source code
get_sim.numeric Man page Source code
get_sim.sim_index Man page Source code
get_sim_grid Man page Source code
get_sim_grid_from_ic Source code
get_sim_grid_from_tsm Source code
get_sim_p Man page Source code
get_sim_p.default Man page Source code
get_sim_p.integer Man page Source code
get_sim_p.matrix Man page Source code
get_sim_p.numeric Man page Source code
get_sim_p.sim_index Man page Source code
get_sim_p_from_ontology Man page Source code
get_similarity_rank_matrix Man page Source code
get_term_set_to_term_sims Man page Source code
get_term_sim_mat Man page Source code
group_sim Source code
lin Man page Source code
lin_asym Source code
ontologySimilarity Man page
ontologySimilarity-package Man page
resnik Man page Source code
resnik_asym Source code
sample_group_sim Man page Source code
sample_group_sim.default Man page Source code
sample_group_sim.integer Man page Source code
sample_group_sim.matrix Man page Source code
sample_group_sim.numeric Man page Source code
sample_group_sim.sim_index Man page Source code
sample_group_sim_from_ontology Man page Source code
sample_null Source code
sim_grid Source code
sim_grid_ic Source code
sim_p Source code

Files

inst
inst/doc
inst/doc/ontologySimilarity-GO-example.R
inst/doc/ontologySimilarity-examples.html
inst/doc/ontologySimilarity-GO-example.Rmd
inst/doc/ontologySimilarity-introduction.html
inst/doc/ontologySimilarity-introduction.Rmd
inst/doc/ontologySimilarity-GO-example.html
inst/doc/ontologySimilarity-introduction.R
inst/doc/ontologySimilarity-examples.Rmd
inst/doc/ontologySimilarity-examples.R
src
src/TermList.cpp
src/TermSetSimData.h
src/Interface.h
src/PVal.cpp
src/Sampling.h
src/SimMatrix.cpp
src/PVal.h
src/RcppExports.cpp
src/TermSetSimData.cpp
src/Sampling.cpp
src/SimMatrix.h
src/Interface.cpp
src/TermList.h
NAMESPACE
data
data/GO_IC.RData
data/gene_GO_terms.RData
R
R/group-sim.R
R/term-set-sim.R
R/data.R
R/functions.R
R/RcppExports.R
vignettes
vignettes/ontologySimilarity-GO-example.Rmd
vignettes/ontologySimilarity-introduction.Rmd
vignettes/ontologySimilarity-examples.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/get_profile_sims.Rd
man/sample_group_sim_from_ontology.Rd
man/gene_GO_terms.Rd
man/get_term_set_to_term_sims.Rd
man/get_sim.Rd
man/get_sim_grid.Rd
man/GO_IC.Rd
man/get_sim_p.Rd
man/descendants_IC.Rd
man/sample_group_sim.Rd
man/get_sim_p_from_ontology.Rd
man/get_asym_sim_grid.Rd
man/get_similarity_rank_matrix.Rd
man/get_term_sim_mat.Rd
man/lin.Rd
man/resnik.Rd
man/ontologySimilarity-package.Rd
man/create_sim_index.Rd
ontologySimilarity documentation built on May 19, 2017, 9:56 p.m.