mgoSim {GOSemSim} | R Documentation |
Given two GO term sets, this function will calculate the semantic similarity between them, and return their semantic similarity
mgoSim(GO1, GO2, ont="MF", organism="human", measure="Wang")
GO1 |
A set of go terms. |
GO2 |
Another set of go terms. |
ont |
One of "MF", "BP", and "CC" subontologies. |
organism |
One of "human", "rat", "mouse", "fly" and "yeast". |
measure |
One of "Resnik", "Lin", "Rel", "Jiang" and "Wang" methods. |
mgoSim |
Semantic similarity. |
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
goSim
geneSim
mgeneSim
clusterSim
mclusterSim
go1 <- c("GO:0004022", "GO:0004024", "GO:0004023") go2 <- c("GO:0009055", "GO:0020037") mgoSim("GO:0003824", go2, measure="Wang") mgoSim(go1, go2, ont="MF", organism="human", measure="Wang")