getGeneFeatures: Get simple feature vector representation of genes
In GOSim: Computation of functional similarities between GO terms and gene products; GO enrichment analysis

Description Usage Arguments Details Value Note Author(s) References See Also Examples

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.

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

`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

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

matrix with rows being genes and columns being GO terms.

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

Holger Froehlich

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

getGeneSimPrototypes, selectPrototypes, getGeneSim, getTermSim, setOntology

1	# see selectPrototypes

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