geneSim {GOSemSim} | R Documentation

## 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, semData, measure = "Wang", drop = "IEA",
      combine = "BMA")

### Arguments

`gene1` | Entrez gene id.
`gene2` | Another entrez gene id.
`semData` | GOSemSimDATA object
`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", "avg", "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

        d <- godata('org.Hs.eg.db', ont="MF", computeIC=FALSE)
    geneSim("241", "251", semData=d, measure="Wang")

[Package GOSemSim version 2.8.0 Index]