GOSemSim (version 1.28.1)

mclusterSim: Pairwise Semantic Similarities for a List of Gene Clusters

Description

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

Usage

mclusterSim(clusters, ont = "MF", organism = "human", measure = "Wang", drop = "IEA", combine = "BMA")

Arguments

clusters

A list of gene clusters.

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

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 mgeneSim clusterSim

Examples

## cluster1 <- c("835", "5261","241")
	## cluster2 <- c("578","582")
	## cluster3 <- c("307", "308", "317")
	## clusters <- list(a=cluster1, b=cluster2, c=cluster3)
	## mclusterSim(clusters, ont="MF", organism="human", measure="Wang")