GOSemSim (version 1.28.1)

goSim: Semantic Similarity Between Two GO Terms

Description

Given two GO IDs, this function calculates their semantic similarity.

Usage

goSim(GOID1, GOID2, ont = "MF", organism = "human", measure = "Wang")

Arguments

GOID1

GO ID 1.

GOID2

GO ID 2.

ont

One of "MF", "BP", and "CC" subontologies.

organism

One of "anopheles", "arabidopsis", "bovine", "canine", "chicken", "chimp", "coelicolor", "ecolik12", "ecsakai", "fly", "human", "malaria", "mouse", "pig", "rat","rhesus", "worm", "xenopus", "yeast" and "zebrafish".

measure

One of "Resnik", "Lin", "Rel", "Jiang" and "Wang" methods.

Value

similarity

References

Yu et al. (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics (Oxford, England), 26:7 976--978, April 2010. ISSN 1367-4803 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976 PMID: 20179076

See Also

mgoSim geneSim mgeneSim clusterSim mclusterSim

Examples

goSim("GO:0004022", "GO:0005515", ont="MF", measure="Wang")