getGeneFeatures {GOSim} | R Documentation

## 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

### 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

    	# see selectPrototypes

[Package GOSim version 1.26.0 Index]