GOSim (version 1.10.0)

getGeneFeatures: Get simple feature vector representation of genes

Description

Computes feature vectors for list of genes: Each gene is represented by a vector describing the presence/absence of all GO terms. The absence of each GO term is additionally weighted by its information content.

Usage

getGeneFeatures(genelist, pca=FALSE, normalization=FALSE, verbose=FALSE)

Arguments

genelist

character vector of Entrez gene IDs

pca

perform PCA on feature vectors to reduce dimensionality

normalization

scale the feature vectors to norm 1

verbose

print out additional information

Value

matrix with rows being genes and columns being GO terms.

Details

The PCA postprocessing determines the principal components that can explain at least 95% of the total variance in the feature space.

References

M. Mistry, P Pavlidis, Gene Ontology term overlap as a measure of gene functional similarity, BMC Bioinformatics, 9:327, 2008.

See Also

getGeneSimPrototypes, selectPrototypes, getGeneSim, getTermSim, setOntology

Examples

	# see selectPrototypes