mgoSim: Semantic Similarity Between two GO terms lists

In YuLab-SMU/GOSemSim: GO-terms Semantic Similarity Measures

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, semData, measure = "Wang", combine = "BMA")

Arguments

GO1	A set of go terms.
GO2	Another set of go terms.
semData	GOSemSimDATA object
measure	One of "Resnik", "Lin", "Rel", "Jiang", "TCSS" and "Wang" methods.
combine	One of "max", "avg", "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

    d <- godata('org.Hs.eg.db', ont="MF", computeIC=FALSE)
go1 <- c("GO:0004022", "GO:0004024", "GO:0004023")
go2 <- c("GO:0009055", "GO:0020037")
mgoSim("GO:0003824", go2, semData=d, measure="Wang")
mgoSim(go1, go2, semData=d, measure="Wang")

YuLab-SMU/GOSemSim documentation built on Nov. 1, 2024, 4:43 a.m.