mgeneSim {GOSemSim} | R Documentation

## Pairwise Semantic Similarity for a List of Genes

### Description

Given a list of genes, this function calculates pairwise semantic similarities.

### Usage

    mgeneSim(
      genes,
      semData,
      measure = "Wang",
      drop = "IEA",
      combine = "BMA",
      verbose = TRUE
    )

### Arguments

`genes` | A list of entrez gene IDs.
`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.
`verbose` | show progress bar or not.

### Value

similarity matrix

### 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` `geneSim` `clusterSim` `mclusterSim`

### Examples

    d <- godata('org.Hs.eg.db', ont="MF", computeIC=FALSE)
    mgeneSim(c("835", "5261","241"), semData=d, measure="Wang")

[Package GOSemSim version 2.12.1 Index]