GOSemSim (version 1.30.2)

mgoSim: Semantic Similarity Between two GO terms lists

Description

Given two GO term sets, this function will calculate the semantic similarity between them, and return their semantic similarity

Usage

mgoSim(GO1, GO2, ont = "MF", organism = "human", measure = "Wang", combine = "BMA")

Arguments

GO1

A set of go terms.

GO2

Another set of go terms.

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.

combine

One of "max", "average", "rcmax", "BMA" methods, for combining semantic similarity scores of multiple GO terms associated with protein or multiple proteins assiciated with protein cluster.

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

goSim geneSim mgeneSim clusterSim mclusterSim

Examples

go1 <- c("GO:0004022", "GO:0004024", "GO:0004023")
go2 <- c("GO:0009055", "GO:0020037")
mgoSim("GO:0003824", go2, measure="Wang")
mgoSim(go1, go2, ont="MF", organism="human", measure="Wang")