GOSemSim (version 1.28.1)

geneSim: Semantic Similarity Between two Genes

Description

Given two genes, this function will calculate the semantic similarity between them, and return their semantic similarity and the corresponding GO terms

Usage

geneSim(gene1, gene2, ont = "MF", organism = "human", measure = "Wang", drop = "IEA", combine = "BMA")

Arguments

gene1

Entrez gene id.

gene2

Another entrez gene id.

ont

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

organism

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

measure

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

drop

A set of evidence codes based on which certain annotations are dropped. Use NULL to keep all GO annotations.

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

list of similarity value and corresponding GO.

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 mgoSim mgeneSim clusterSim mclusterSim

Examples

geneSim("241", "251", ont="MF", organism="human", measure="Wang")