mclusterSim {GOSemSim}R Documentation

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")

Arguments

clusters A list of gene clusters.
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

simmat A Matrix of Pairwise Semantic Similarities

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{clusterSim}

Examples

        cluster1 <- c("snR67","snR40","snR48", "snR17a","snR8")
        cluster2 <- c("YOR251C", "YPR137C-B", "YPR010C", "YPR072W")
        cluster3 <- c("YNL133C", "YOL041C", "YOL018C", "YOR236W", "YOR179C", "YOR230W")
        clusters <- list(a=cluster1, b=cluster2, c=cluster3)
        mclusterSim(clusters, ont="MF", organism="yeast", measure="Wang")

[Package GOSemSim version 1.2.0 Index]