GOSemSim (version 1.30.2)

mgeneSim: Pairwise Semantic Similarity for a List of Genes

Description

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

Usage

mgeneSim(genes, ont = "MF", organism = "human", measure = "Wang", drop = "IEA", combine = "BMA", verbose = TRUE)

Arguments

genes

A list of entrez gene IDs.

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.

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

mgeneSim(c("835", "5261","241"), ont="MF", organism="human", measure="Wang")