getGeneSim {GOSim} | R Documentation |
Calculate the pairwise functional similarities for a list of genes using different strategies.
getGeneSim(genelist, similarity = "OA", similarityTerm = "JiangConrath", normalization = TRUE, verbose = TRUE)
genelist |
character vector of Entrez gene IDs |
similarity |
method to calculate the functional similarity between gene products |
similarityTerm |
method to compute the similarity of GO terms |
normalization |
normalize the similarities to [0,1] by transforming sim(x,y) <- sim(x,y)/sqrt(sim(x,x)*sim(y,y)) |
verbose |
print out some information |
The method to calculate the pairwise functional similarity between gene products can either be: begin{ldescription}
n x n similarity matrix (n = number of genes)
The result depends on the currently set ontology.
Holger Froehlich
H. Froehlich, N. Speer, C. Spieth, and A. Zell, Kernel Based Functional Gene Grouping, Proc. Int. Joint Conf. on Neural Networks (IJCNN), 6886 - 6891, 2006
getGeneSimPrototypes
, getTermSim
, setOntology
# see evaluateClustering