clusterSim {GOSemSim}R Documentation

Semantic Similarity Between Two Gene Clusters

Description

Given two gene clusters, this function calculates semantic similarity between them.

Usage

clusterSim(cluster1, cluster2, ont = "MF",  organism="human", measure="Wang", drop= "IEA")

Arguments

cluster1 A set of gene IDs.
cluster2 Another set of gene IDs.
ont One of "MF", "BP", and "CC" subontologies.
measure One of "Resnik", "Lin", "Rel", "Jiang" and "Wang" methods.
organism One of "human", "rat", "mouse", "fly" and "yeast".
drop A set of evidence codes based on which certain annotations are dropped. Use NULL to keep all GO annotations.

Value

sim Semantic Similarity.

References

Wang et al.(2007) A new method to measure the semantic similarity of go terms Bioinformatics (Oxford, England), 23:0 1274–81, May 2007. ISSN 1460-2059 http://www.ncbi.nlm.nih.gov/pubmed/17344234 PMID: 17344234

P W Lord et al.(2003) Semantic similarity measures as tools for exploring the gene ontology Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing, 2003:601-12, ISSN 1793-5091 http://www.ncbi.nlm.nih.gov/pubmed/12603061 PMID: 12603061

See Also

goSim mgoSim geneSim mgeneSim \linke{mclusterSim}

Examples

        cluster1 <- c("snR67","snR40","snR48", "snR17a","snR8")
        cluster2 <- c("YOR251C", "YPR137C-B", "YPR010C", "YPR072W")
        clusterSim(cluster1, cluster2, ont="MF", organism="yeast", measure="Wang")

[Package GOSemSim version 1.2.0 Index]