mclusterSim {GOSemSim} | R Documentation |
Given a list of gene clusters, this function calculates pairwise semantic similarities.
mclusterSim(clusters, ont = "MF", organism="human", measure="Wang", drop= "IEA")
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. |
simmat |
A Matrix of Pairwise Semantic Similarities |
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
geneSim
mgeneSim
\linke{clusterSim}
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")