getGeneSimPrototypes {GOSim}R Documentation

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 = TRUE) 

Arguments

genelist character vector of Entrez gene IDs
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

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.

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

Note

The result depends on the currently set ontology ("BP","MF","CC").

Author(s)

Holger Froehlich

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

 ## Not run: 
 may take some time ...
 proto=selectPrototypes(n=50) # --> returns a character vector of 50 genes with the highest number of annotations
 getGeneSimPrototypes(c("207","208","360"),prototypes=proto, similarityTerm="Resnik")
## End(Not run)

[Package GOSim version 1.2 Index]