GOSim (version 1.10.0)

getGeneSimPrototypes: Compute functional similarity of genes with respect to a feature vector representation.

Description

Computes the pairwise functional similarities for a list of genes: Each gene is represented by a feature vector containing the gene's similarities to predefined prototype genes.

Usage

getGeneSimPrototypes(genelist, prototypes = NULL, similarity = "max", similarityTerm = "JiangConrath", pca = TRUE, normalization = TRUE, verbose = FALSE)

Arguments

genelist

character vector of primary gene IDs according to organism annotation package (see setEvidenceLevel)

prototypes

character vector of Entrez gene IDs representing the prototypes

similarity

method to calculate the similarity to prototypes

similarityTerm

method to compute the GO term similarity

pca

perform PCA on feature vectors to reduce dimensionality

normalization

normalize similarities to [0,1]: sim(x,y) <- 0.5*(sim(x,y)/sqrt(sim(x,x)*sim(y,y)) + 1)

verbose

print additional information

Value

List with items

"similarity"

n x n similarity matrix (n = number of genes)

"prototypes"

prototypes (= prinicipal components, if PCA has been performed)

"features"

feature vectors for each gene: n x d data matrix

Details

The method calls getGeneFeaturesPrototypes to calculate the feature vectors. The functional similarity between two genes is essentially given by the dot product between their feature vectors.

References

[1] 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

[2] N. Speer, H. Froehlich, A. Zell, Functional Grouping of Genes Using Spectral Clustering and Gene Ontology, Proc. Int. Joint Conf. on Neural Networks (IJCNN), pp. 298 - 303, 2005

See Also

getGeneFeaturesPrototypes, selectPrototypes, getGeneSim, getTermSim, setOntology

Examples

#\donttest{ may take some time ...
 proto=selectPrototypes(n=5) # --> returns a character vector of 5 genes with the highest number of annotations
 getGeneSimPrototypes(c("207","208"),prototypes=proto, similarityTerm="Resnik")
#}