geneSim {GOSemSim} | R Documentation |
Given two genes, this function will calculate the semantic similarity between them, and return their semantic similarity and the corresponding GO terms
geneSim(gene1, gene2, ont = "MF", organism="human",measure="Wang", drop= "IEA")
gene1 |
Entrez gene id. |
gene2 |
Another entrez gene id. |
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. |
drop |
A set of evidence codes based on which certain annotations are dropped. Use NULL to keep all GO annotations. |
geneSim |
Semantic similarity. |
GO1 |
Corresponding GO terms for gene1. |
GO2 |
Corresponding GO terms for gene2. |
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
mgoSim
mgeneSim
clusterSim
mclusterSim
geneSim("241", "2561", ont="MF", organism="human", measure="Wang") geneSim("snR18", "YPR062W", ont="MF", organism="yeast", measure="Wang")