getGeneFeatures: Get simple feature vector representation of genes

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

View source: R/geneSimilarity.R

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

1
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

Details

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

Value

matrix with rows being genes and columns being GO terms.

Note

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

Author(s)

Holger Froehlich

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

1
	# see selectPrototypes

GOSim documentation built on Nov. 1, 2018, 2:26 a.m.